-
1
-
-
0037008160
-
Approaches to the Description and Drediction of the Binding Affinity of Small-molecule Ligands to Macromolecular Receptors
-
Gohlke, H.; Klebe, G. Approaches to the Description and Drediction of the Binding Affinity of Small-molecule Ligands to Macromolecular Receptors Angew. Chem., Int. Ed. 2002, 41, 2644-2676 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
2
-
-
33749260698
-
A Critical Assessment of Docking Programs and Scoring Functions
-
Warren, G. L.; Andrews, C. W.; Capelli, A.-M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S. et al. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931 10.1021/jm050362n
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
-
3
-
-
67650097331
-
Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy
-
Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy J. Chem. Inf. Model. 2009, 49, 1455-1474 10.1021/ci900056c
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
4
-
-
0242696091
-
Free Energy Calculations and Ligand Binding
-
Brandsdal, B. O.; Österberg, F.; Almlöf, M.; Feierberg, I.; Luzhkov, V. B.; Åqvist, J. Free Energy Calculations and Ligand Binding Adv. Protein Chem. 2003, 66, 123-158 10.1016/S0065-3233(03)66004-3
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 123-158
-
-
Brandsdal, B.O.1
Österberg, F.2
Almlöf, M.3
Feierberg, I.4
Luzhkov, V.B.5
Åqvist, J.6
-
5
-
-
0034521981
-
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W. et al. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897 10.1021/ar000033j
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
-
6
-
-
84904130280
-
Practical Aspects of Free-Energy Calculations: A Review
-
Hansen, N.; van Gunsteren, W. F. Practical Aspects of Free-Energy Calculations: A Review J. Chem. Theory Comput. 2014, 10, 2632-2647 10.1021/ct500161f
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 2632-2647
-
-
Hansen, N.1
Van Gunsteren, W.F.2
-
7
-
-
84871960256
-
Perspective: Alchemical Free Energy Calculations for Drug Discovery
-
Mobley, D. L.; Klimovich, P. V. Perspective: Alchemical Free Energy Calculations for Drug Discovery J. Chem. Phys. 2012, 137, 230901 10.1063/1.4769292
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 230901
-
-
Mobley, D.L.1
Klimovich, P.V.2
-
8
-
-
33646875701
-
Quantum Mechanics in Structure-Based Drug Design
-
Peters, M. B.; Raha, K.; Merz, K. M. Quantum Mechanics in Structure-Based Drug Design Curr. Opin. Drug Discovery Dev. 2006, 9, 370-379
-
(2006)
Curr. Opin. Drug Discovery Dev.
, vol.9
, pp. 370-379
-
-
Peters, M.B.1
Raha, K.2
Merz, K.M.3
-
9
-
-
33749830966
-
Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design
-
Cavalli, A.; Carloni, P.; Recanatini, M. Target-Related Applications of First Principles Quantum Chemical Methods in Drug Design Chem. Rev. 2006, 106, 3497-3519 10.1021/cr050579p
-
(2006)
Chem. Rev.
, vol.106
, pp. 3497-3519
-
-
Cavalli, A.1
Carloni, P.2
Recanatini, M.3
-
10
-
-
34548430376
-
The Role of Quantum Mechanics in Structure-Based Drug Design
-
Raha, K.; Peters, M. B.; Wang, B.; Yu, N.; Wollacott, A. M.; Westerhoff, L. M.; Merz, K. M. The Role of Quantum Mechanics in Structure-Based Drug Design Drug Discovery Today 2007, 12, 725-731 10.1016/j.drudis.2007.07.006
-
(2007)
Drug Discovery Today
, vol.12
, pp. 725-731
-
-
Raha, K.1
Peters, M.B.2
Wang, B.3
Yu, N.4
Wollacott, A.M.5
Westerhoff, L.M.6
Merz, K.M.7
-
11
-
-
65349110014
-
QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? J. Chem
-
Gleeson, M. P.; Gleeson, D. QM/MM Calculations in Drug Discovery: A Useful Method for Studying Binding Phenomena? J. Chem J. Chem. Inf. Model. 2009, 49, 670-677 10.1021/ci800419j
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 670-677
-
-
Gleeson, M.P.1
Gleeson, D.2
-
12
-
-
77949345617
-
Quantum Mechanical Methods for Drug Design
-
Zhou, T.; Huang, D.; Caflisch, A. Quantum Mechanical Methods for Drug Design Curr. Top. Med. Chem. 2010, 10, 33-45 10.2174/156802610790232242
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 33-45
-
-
Zhou, T.1
Huang, D.2
Caflisch, A.3
-
13
-
-
77949343956
-
QM/MM Approaches in Medicinal Chemistry Research
-
Menikarachchi, L. C.; Gascón, J. A. QM/MM Approaches in Medicinal Chemistry Research Curr. Top. Med. Chem. 2010, 10, 46-54 10.2174/156802610790232297
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 46-54
-
-
Menikarachchi, L.C.1
Gascón, J.A.2
-
14
-
-
77954027036
-
Estimates of Ligand-Binding Affinities Supported by Quantum Mechanical Methods
-
Söderhjelm, P.; Kongsted, J.; Genheden, S.; Ryde, U. Estimates of Ligand-Binding Affinities Supported by Quantum Mechanical Methods Interdiscip. Sci.: Comput. Life Sci. 2010, 2, 21-37 10.1007/s12539-010-0083-0
-
(2010)
Interdiscip. Sci.: Comput. Life Sci.
, vol.2
, pp. 21-37
-
-
Söderhjelm, P.1
Kongsted, J.2
Genheden, S.3
Ryde, U.4
-
15
-
-
73649093135
-
Quantum Mechanical Effect in Protein-Ligand Interaction
-
Jing, Y.-Q.; Han, K.-L. Quantum Mechanical Effect in Protein-Ligand Interaction Expert Opin. Drug Discovery 2010, 5, 33-49 10.1517/17460440903440127
-
(2010)
Expert Opin. Drug Discovery
, vol.5
, pp. 33-49
-
-
Jing, Y.-Q.1
Han, K.-L.2
-
16
-
-
79955045990
-
Bridging Quantum Mechanics and Structure-Based Drug Design
-
De Vivo, M. Bridging Quantum Mechanics and Structure-Based Drug Design Front. Biosci., Landmark Ed. 2011, 16, 1619-1626 10.2741/3809
-
(2011)
Front. Biosci., Landmark Ed.
, vol.16
, pp. 1619-1626
-
-
De Vivo, M.1
-
17
-
-
1042292416
-
Quantum Mechanics in Structure-Based Ligand Design
-
Gohlke, H. Methods and Principles in Medicinal Chemistry, Vol. Wiley-VCH Verlag: Weinheim, Germany
-
Söderhjelm, P.; Genheden, S.; Ryde, U. Quantum Mechanics in Structure-Based Ligand Design. In Protein-Ligand Interactions; Gohlke, H., Ed.; Methods and Principles in Medicinal Chemistry, Vol. 53; Wiley-VCH Verlag: Weinheim, Germany, 2012; pp 121-143.
-
(2012)
Protein-Ligand Interactions
, vol.53
, pp. 121-143
-
-
Söderhjelm, P.1
Genheden, S.2
Ryde, U.3
-
18
-
-
84861164295
-
The Increasing Role of QM/MM in Drug Discovery
-
Lodola, A.; De Vivo, M. The Increasing Role of QM/MM in Drug Discovery Adv. Protein Chem. Struct. Biol. 2012, 87, 337-362 10.1016/B978-0-12-398312-1.00011-1
-
(2012)
Adv. Protein Chem. Struct. Biol.
, vol.87
, pp. 337-362
-
-
Lodola, A.1
De Vivo, M.2
-
19
-
-
84883853834
-
The Semiempirical Quantum Mechanical Scoring Function for in Silico Drug Design
-
Lepsík, M.; Rezác, J.; Kolár, M.; Pecina, A.; Hobza, P.; Fanfrlík, J. The Semiempirical Quantum Mechanical Scoring Function for in Silico Drug Design ChemPlusChem 2013, 78, 921-931 10.1002/cplu.201300199
-
(2013)
ChemPlusChem
, vol.78
, pp. 921-931
-
-
Lepsík, M.1
Rezác, J.2
Kolár, M.3
Pecina, A.4
Hobza, P.5
Fanfrlík, J.6
-
20
-
-
84874310966
-
The Application of Quantum Mechanics in Structure-Based Drug Design
-
Mucs, D.; Bryce, R. A. The Application of Quantum Mechanics in Structure-Based Drug Design Expert Opin. Drug Discovery 2013, 8, 263-276 10.1517/17460441.2013.752812
-
(2013)
Expert Opin. Drug Discovery
, vol.8
, pp. 263-276
-
-
Mucs, D.1
Bryce, R.A.2
-
21
-
-
84881343069
-
Drug Design for Protein Kinases and Phosphatases: Flexible-Receptor Docking, Binding Affinity and Specificity, and Drug-Binding Kinetics
-
Wong, C. F.; Bairy, S. Drug Design for Protein Kinases and Phosphatases: Flexible-Receptor Docking, Binding Affinity and Specificity, and Drug-Binding Kinetics Curr. Pharm. Des. 2013, 19, 4739-4754 10.2174/1381612811319260006
-
(2013)
Curr. Pharm. Des.
, vol.19
, pp. 4739-4754
-
-
Wong, C.F.1
Bairy, S.2
-
22
-
-
84877582393
-
Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics
-
Ilatovskiy, A. V.; Abagyan, R.; Kufareva, I. Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics Int. J. Quantum Chem. 2013, 113, 1669-1675 10.1002/qua.24400
-
(2013)
Int. J. Quantum Chem.
, vol.113
, pp. 1669-1675
-
-
Ilatovskiy, A.V.1
Abagyan, R.2
Kufareva, I.3
-
23
-
-
79955980720
-
Physics-Based Scoring of Protein-Ligand Interactions: Explicit Polarizability, Quantum Mechanics and Free Energies
-
Bryce, R. A. Physics-Based Scoring of Protein-Ligand Interactions: Explicit Polarizability, Quantum Mechanics and Free Energies Future Med. Chem. 2011, 3, 683-698 10.4155/fmc.11.30
-
(2011)
Future Med. Chem.
, vol.3
, pp. 683-698
-
-
Bryce, R.A.1
-
24
-
-
84903690739
-
Quantum Chemical Approaches: Semiempirical Molecular Orbital and Hybrid Quantum Mechanical/Molecular Mechanical Techniques
-
Bryce, R. A.; Hillier, I. H. Quantum Chemical Approaches: Semiempirical Molecular Orbital and Hybrid Quantum Mechanical/Molecular Mechanical Techniques Curr. Pharm. Des. 2014, 20, 3293-3302 10.2174/13816128113199990601
-
(2014)
Curr. Pharm. Des.
, vol.20
, pp. 3293-3302
-
-
Bryce, R.A.1
Hillier, I.H.2
-
25
-
-
84903713248
-
Free Energy Calculations to Estimate Ligand-Binding Affinities in Structure-Based Drug Design
-
Reddy, M. R.; Reddy, C. R.; Rathore, R. S.; Erion, M. D.; Aparoy, P.; Reddy, R. N.; Reddanna, P. Free Energy Calculations to Estimate Ligand-Binding Affinities in Structure-Based Drug Design Curr. Pharm. Des. 2014, 20, 3323-3341 10.2174/13816128113199990604
-
(2014)
Curr. Pharm. Des.
, vol.20
, pp. 3323-3341
-
-
Reddy, M.R.1
Reddy, C.R.2
Rathore, R.S.3
Erion, M.D.4
Aparoy, P.5
Reddy, R.N.6
Reddanna, P.7
-
26
-
-
84929192572
-
Predicting Accurate Absolute Binding Energies in Aqueous Solution: Thermodynamic Considerations for Electronic Structure Methods
-
Jensen, J. H. Predicting Accurate Absolute Binding Energies in Aqueous Solution: Thermodynamic Considerations for Electronic Structure Methods Phys. Chem. Chem. Phys. 2015, 17, 12441-12451 10.1039/C5CP00628G
-
(2015)
Phys. Chem. Chem. Phys.
, vol.17
, pp. 12441-12451
-
-
Jensen, J.H.1
-
27
-
-
67650547195
-
Conformational Variability of Benzamidinium-Based Inhibitors
-
Li, X.; He, X.; Wang, B.; Merz, K. Conformational Variability of Benzamidinium-Based Inhibitors J. Am. Chem. Soc. 2009, 131, 7742-7754 10.1021/ja9010833
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 7742-7754
-
-
Li, X.1
He, X.2
Wang, B.3
Merz, K.4
-
28
-
-
20344403522
-
Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach
-
Cho, A. E.; Guallar, V.; Berne, B. J.; Friesner, R. Importance of Accurate Charges in Molecular Docking: Quantum Mechanical/Molecular Mechanical (QM/MM) Approach J. Comput. Chem. 2005, 26, 915-931 10.1002/jcc.20222
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 915-931
-
-
Cho, A.E.1
Guallar, V.2
Berne, B.J.3
Friesner, R.4
-
29
-
-
33750467966
-
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
-
Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field J. Med. Chem. 2006, 49, 6596-6606 10.1021/jm0608210
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Söderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
30
-
-
64549135080
-
Conformational Dependence of Charges in Protein Simulations
-
Söderhjelm, P.; Ryde, U. Conformational Dependence of Charges in Protein Simulations J. Comput. Chem. 2009, 30, 750-760 10.1002/jcc.21097
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 750-760
-
-
Söderhjelm, P.1
Ryde, U.2
-
31
-
-
84857277947
-
Transferability of Conformational Dependent Charges from Protein Simulations
-
Genheden, S.; Söderhjelm, P.; Ryde, U. Transferability of Conformational Dependent Charges From Protein Simulations Int. J. Quantum Chem. 2012, 112, 1768-1785 10.1002/qua.22967
-
(2012)
Int. J. Quantum Chem.
, vol.112
, pp. 1768-1785
-
-
Genheden, S.1
Söderhjelm, P.2
Ryde, U.3
-
32
-
-
39749175582
-
Receptor-Specific Scoring Functions Derived from Quantum Chemical Models Improve Affinity Estimates for in-Silico Drug Discovery
-
Fischer, B.; Fukuzawa, K.; Wenzel, W. Receptor-Specific Scoring Functions Derived From Quantum Chemical Models Improve Affinity Estimates for in-Silico Drug Discovery Proteins: Struct., Funct., Genet. 2008, 70, 1264-1273 10.1002/prot.21607
-
(2008)
Proteins: Struct., Funct., Genet.
, vol.70
, pp. 1264-1273
-
-
Fischer, B.1
Fukuzawa, K.2
Wenzel, W.3
-
33
-
-
84879596436
-
Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization
-
Liu, J.; He, X.; Zhang, J. Z. H. Improving the Scoring of Protein-Ligand Binding Affinity by Including the Effects of Structural Water and Electronic Polarization J. Chem. Inf. Model. 2013, 53, 1306-1314 10.1021/ci400067c
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1306-1314
-
-
Liu, J.1
He, X.2
Zhang, J.Z.H.3
-
34
-
-
84954382352
-
Thermodynamics Calculation of Protein-Ligand Interactions by QM/MM Polarizable Charge Parameters
-
Wang, J.; Shao, Q.; Cossins, B. P.; Shi, J.; Chen, K.; Zhu, W. Thermodynamics Calculation of Protein-Ligand Interactions by QM/MM Polarizable Charge Parameters J. Biomol. Struct. Dyn. 2016, 34, 163-176 10.1080/07391102.2015.1019928
-
(2016)
J. Biomol. Struct. Dyn.
, vol.34
, pp. 163-176
-
-
Wang, J.1
Shao, Q.2
Cossins, B.P.3
Shi, J.4
Chen, K.5
Zhu, W.6
-
35
-
-
84920989305
-
Comparative Analysis of Various Electrostatic Potentials on Docking Precision Against Cyclin-Dependent Kinase 2 Protein: A Multiple Docking Approach
-
Tripathi, S. K.; Soundarya, R. N.; Singh, P.; Singh, S. K. Comparative Analysis of Various Electrostatic Potentials on Docking Precision Against Cyclin-Dependent Kinase 2 Protein: A Multiple Docking Approach Chem. Biol. Drug Des. 2015, 85, 107-118 10.1111/cbdd.12376
-
(2015)
Chem. Biol. Drug Des.
, vol.85
, pp. 107-118
-
-
Tripathi, S.K.1
Soundarya, R.N.2
Singh, P.3
Singh, S.K.4
-
36
-
-
0001728908
-
Quantum-Chemical Descriptors in QSAR/QSPR Studies
-
Karelson, M.; Lobanov, V. S.; Katritzky, A. R. Quantum-Chemical Descriptors in QSAR/QSPR Studies Chem. Rev. 1996, 96, 1027-1044 10.1021/cr950202r
-
(1996)
Chem. Rev.
, vol.96
, pp. 1027-1044
-
-
Karelson, M.1
Lobanov, V.S.2
Katritzky, A.R.3
-
37
-
-
59149086030
-
Applications of 2D Descriptors in Drug Design: A Dragon Tale
-
Helguera, A. M.; Combes, R. D.; Gonzalez, M. P.; Cordeiro, M. N. D. S. Applications of 2D Descriptors in Drug Design: A Dragon Tale Curr. Top. Med. Chem. 2008, 8, 1628-1655 10.2174/156802608786786598
-
(2008)
Curr. Top. Med. Chem.
, vol.8
, pp. 1628-1655
-
-
Helguera, A.M.1
Combes, R.D.2
Gonzalez, M.P.3
Cordeiro, M.N.D.S.4
-
38
-
-
84919388001
-
Multiscale Quantum Chemical Approaches to QSAR Modeling and Drug Design
-
De Benedetti, P. G.; Fanelli, F. Multiscale Quantum Chemical Approaches to QSAR Modeling and Drug Design Drug Discovery Today 2014, 19, 1921-1927 10.1016/j.drudis.2014.09.024
-
(2014)
Drug Discovery Today
, vol.19
, pp. 1921-1927
-
-
De Benedetti, P.G.1
Fanelli, F.2
-
39
-
-
75749153258
-
Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM
-
Alzate-Morales, J.; Caballero, J. Computational Study of the Interactions between Guanine Derivatives and Cyclin-Dependent Kinase 2 (CDK2) by CoMFA and QM/MM J. Chem. Inf. Model. 2010, 50, 110-122 10.1021/ci900302z
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 110-122
-
-
Alzate-Morales, J.1
Caballero, J.2
-
40
-
-
84879566082
-
Quantum Mechanics-Based Properties for 3D-QSAR
-
El Kerdawy, A.; Güssregen, S.; Matter, H.; Hennemann, M.; Clark, T. Quantum Mechanics-Based Properties for 3D-QSAR J. Chem. Inf. Model. 2013, 53, 1486-1502 10.1021/ci400181b
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 1486-1502
-
-
El Kerdawy, A.1
Güssregen, S.2
Matter, H.3
Hennemann, M.4
Clark, T.5
-
42
-
-
84898005451
-
Quantum Chemical Studies of Mechanisms for Metalloenzymes
-
Blomberg, M. R. A.; Borowski, T.; Himo, F.; Liao, R.-Z.; Siegbahn, P. E. M. Quantum Chemical Studies of Mechanisms for Metalloenzymes Chem. Rev. 2014, 114, 3601-3658 10.1021/cr400388t
-
(2014)
Chem. Rev.
, vol.114
, pp. 3601-3658
-
-
Blomberg, M.R.A.1
Borowski, T.2
Himo, F.3
Liao, R.-Z.4
Siegbahn, P.E.M.5
-
43
-
-
67649476220
-
Recent Developments of the Quantum Chemical Cluster Approach for Modeling Enzyme Reactions
-
Siegbahn, P. E. M.; Himo, F. Recent Developments of the Quantum Chemical Cluster Approach for Modeling Enzyme Reactions JBIC, J. Biol. Inorg. Chem. 2009, 14, 643-651 10.1007/s00775-009-0511-y
-
(2009)
JBIC, J. Biol. Inorg. Chem.
, vol.14
, pp. 643-651
-
-
Siegbahn, P.E.M.1
Himo, F.2
-
44
-
-
60349127442
-
QM/MM Methods for Biomolecular Systems
-
Senn, H. M.; Thiel, W. QM/MM Methods for Biomolecular Systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229 10.1002/anie.200802019
-
(2009)
Angew. Chem., Int. Ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
45
-
-
33846570818
-
QM/MM: What Have We Learned, Where Are We, and Where Do We Go from Here?
-
Lin, H.; Truhlar, D. G. QM/MM: What Have We Learned, Where Are We, and Where Do We Go From Here? Theor. Chem. Acc. 2007, 117, 185-199 10.1007/s00214-006-0143-z
-
(2007)
Theor. Chem. Acc.
, vol.117
, pp. 185-199
-
-
Lin, H.1
Truhlar, D.G.2
-
48
-
-
84956767824
-
The Wave Mechanics of an Atom with a Non-Coulomb Central Field. Part I. Theory and Methods
-
Hartree, D. R. The Wave Mechanics of an Atom with a Non-Coulomb Central Field. Part I. Theory and Methods Math. Proc. Cambridge Philos. Soc. 1928, 24, 89-132 10.1017/S0305004100011919
-
(1928)
Math. Proc. Cambridge Philos. Soc.
, vol.24
, pp. 89-132
-
-
Hartree, D.R.1
-
49
-
-
0043231529
-
Selfconsistent Field mit Austausch für Natrium
-
Fock, V. Selfconsistent Field mit Austausch für Natrium Eur. Phys. J. A 1930, 62, 795-805 10.1007/BF01330439
-
(1930)
Eur. Phys. J. A
, vol.62
, pp. 795-805
-
-
Fock, V.1
-
50
-
-
6944251055
-
Note on an Approximation Treatment for Many-Electron Systems
-
Møller, C.; Plesset, M. S. Note on an Approximation Treatment for Many-Electron Systems Phys. Rev. 1934, 46, 618-622 10.1103/PhysRev.46.618
-
(1934)
Phys. Rev.
, vol.46
, pp. 618-622
-
-
Møller, C.1
Plesset, M.S.2
-
51
-
-
0006244148
-
A Fifth-Order Perturbation Comparison of Electron Correlation Theories
-
Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. A Fifth-Order Perturbation Comparison of Electron Correlation Theories Chem. Phys. Lett. 1989, 157, 479-483 10.1016/S0009-2614(89)87395-6
-
(1989)
Chem. Phys. Lett.
, vol.157
, pp. 479-483
-
-
Raghavachari, K.1
Trucks, G.W.2
Pople, J.A.3
Head-Gordon, M.4
-
52
-
-
84893773262
-
Semiempirical Quantum-Chemical Methods
-
Thiel, W. Semiempirical Quantum-Chemical Methods WIREs Comput. Mol. Sci. 2014, 4, 145-157 10.1002/wcms.1161
-
(2014)
WIREs Comput. Mol. Sci.
, vol.4
, pp. 145-157
-
-
Thiel, W.1
-
53
-
-
0842341771
-
AM1: A New General Purpose Quantum Mechanical Molecular Model
-
Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: A New General Purpose Quantum Mechanical Molecular Model J. Am. Chem. Soc. 1985, 107, 3902-3909 10.1021/ja00299a024
-
(1985)
J. Am. Chem. Soc.
, vol.107
, pp. 3902-3909
-
-
Dewar, M.J.S.1
Zoebisch, E.G.2
Healy, E.F.3
Stewart, J.J.P.4
-
54
-
-
33745597056
-
-
Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. J. Comput. Chem. 2006, 27, 1101 10.1002/jcc.20425
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1101
-
-
Rocha, G.B.1
Freire, R.O.2
Simas, A.M.3
Stewart, J.J.P.4
-
55
-
-
84988129057
-
Optimization of Parameters for Semiempirical Methods I. Method
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods I. Method J. Comput. Chem. 1989, 10, 209-220 10.1002/jcc.540100208
-
(1989)
J. Comput. Chem.
, vol.10
, pp. 209-220
-
-
Stewart, J.J.P.1
-
56
-
-
0036889839
-
PDDG/PM3 and PDDG/MNDO: Improved Semiempirical Methods
-
Repasky, M. P.; Chandrasekhar, J.; Jorgensen, W. L. PDDG/PM3 and PDDG/MNDO: Improved Semiempirical Methods J. Comput. Chem. 2002, 23, 1601-1622 10.1002/jcc.10162
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1601-1622
-
-
Repasky, M.P.1
Chandrasekhar, J.2
Jorgensen, W.L.3
-
57
-
-
35448937584
-
Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements
-
Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213 10.1007/s00894-007-0233-4
-
(2007)
J. Mol. Model.
, vol.13
, pp. 1173-1213
-
-
Stewart, J.J.P.1
-
58
-
-
0034389977
-
Orthogonalization Corrections for Semiempirical Methods
-
Weber, W.; Thiel, W. Orthogonalization Corrections for Semiempirical Methods Theor. Chem. Acc. 2000, 103, 495-506 10.1007/s002149900083
-
(2000)
Theor. Chem. Acc.
, vol.103
, pp. 495-506
-
-
Weber, W.1
Thiel, W.2
-
59
-
-
67849101722
-
Semiempirical Quantum Chemical PM6Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
-
Rezác, J.; Fanfrlík, J.; Salahub, D.; Hobza, P. Semiempirical Quantum Chemical PM6Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes J. Chem. Theory Comput. 2009, 5, 1749-1760 10.1021/ct9000922
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1749-1760
-
-
Rezác, J.1
Fanfrlík, J.2
Salahub, D.3
Hobza, P.4
-
60
-
-
77950139248
-
A Transferable H-Bond Correction for Semiempirical Quantum-Chemical Methods
-
Korth, M.; Pitonák, M.; Rezác, J.; Hobza, P. A Transferable H-Bond Correction for Semiempirical Quantum-Chemical Methods J. Chem. Theory Comput. 2010, 6, 344-352 10.1021/ct900541n
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 344-352
-
-
Korth, M.1
Pitonák, M.2
Rezác, J.3
Hobza, P.4
-
61
-
-
79954583073
-
A Halogen-Bonding Correction for the Semiempirical PM6Method
-
Rezác, J.; Hobza, P. A Halogen-Bonding Correction for the Semiempirical PM6Method Chem. Phys. Lett. 2011, 506, 286-289 10.1016/j.cplett.2011.03.009
-
(2011)
Chem. Phys. Lett.
, vol.506
, pp. 286-289
-
-
Rezác, J.1
Hobza, P.2
-
62
-
-
84855668199
-
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
-
Rezác, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods J. Chem. Theory Comput. 2012, 8, 141-151 10.1021/ct200751e
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 141-151
-
-
Rezác, J.1
Hobza, P.2
-
63
-
-
10644250257
-
Inhomogeneous Electron Gas
-
Hohenberg, P.; Kohn, W. Inhomogeneous Electron Gas Phys. Rev. 1964, 136, B864-B871 10.1103/PhysRev.136.B864
-
(1964)
Phys. Rev.
, vol.136
, pp. B864-B871
-
-
Hohenberg, P.1
Kohn, W.2
-
64
-
-
0042113153
-
Self-Consistent Equations Including Exchange and Correlation Effects
-
Kohn, W.; Sham, L. J. Self-Consistent Equations Including Exchange and Correlation Effects Phys. Rev. 1965, 140, A1133-A1138 10.1103/PhysRev.140.A1133
-
(1965)
Phys. Rev.
, vol.140
, pp. A1133-A1138
-
-
Kohn, W.1
Sham, L.J.2
-
65
-
-
4243553426
-
Density-functional Exchange-Energy Approximation with Correct Asymptotic Behavior
-
Becke, A. D. Density-functional Exchange-Energy Approximation with Correct Asymptotic Behavior Phys. Rev. A: At., Mol., Opt. Phys. 1988, 38, 3098-3100 10.1103/PhysRevA.38.3098
-
(1988)
Phys. Rev. A: At., Mol., Opt. Phys.
, vol.38
, pp. 3098-3100
-
-
Becke, A.D.1
-
66
-
-
5944261746
-
Density-functional Approximation for the Correlation Energy of the Inhomogeneous Electron Gas
-
Perdew, J. P. Density-functional Approximation for the Correlation Energy of the Inhomogeneous Electron Gas Phys. Rev. B: Condens. Matter Mater. Phys. 1986, 33, 8822-8824 10.1103/PhysRevB.33.8822
-
(1986)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.33
, pp. 8822-8824
-
-
Perdew, J.P.1
-
67
-
-
4243943295
-
Generalized Gradient Approximation Made Simple
-
Perdew, J. P.; Burke, K.; Ernzerhof, M. Generalized Gradient Approximation Made Simple Phys. Rev. Lett. 1996, 77, 3865-3868 10.1103/PhysRevLett.77.3865
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 3865-3868
-
-
Perdew, J.P.1
Burke, K.2
Ernzerhof, M.3
-
68
-
-
0242593713
-
Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids
-
Tao, J.; Perdew, J. P.; Staroverov, V. N.; Scuseria, G. E. Climbing the Density Functional Ladder: Nonempirical Meta-Generalized Gradient Approximation Designed for Molecules and Solids Phys. Rev. Lett. 2003, 91, 146401 10.1103/PhysRevLett.91.146401
-
(2003)
Phys. Rev. Lett.
, vol.91
, pp. 146401
-
-
Tao, J.1
Perdew, J.P.2
Staroverov, V.N.3
Scuseria, G.E.4
-
69
-
-
43049141516
-
The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals
-
Zhao, Y.; Truhlar, D. G. The M06 Suite of Density Functionals for Main Group Thermochemistry, Thermochemical Kinetics, Noncovalent Interactions, Excited States, and Transition Elements: Two New Functionals and Systematic Testing of Four M06-Class Functionals and 12 Other Functionals Theor. Chem. Acc. 2008, 120, 215-241 10.1007/s00214-007-0310-x
-
(2008)
Theor. Chem. Acc.
, vol.120
, pp. 215-241
-
-
Zhao, Y.1
Truhlar, D.G.2
-
70
-
-
11244326290
-
Exchange Functionals with Improved Longrange Behavior and Adiabatic Connection Methods without Adjustable Parameters: The Mpw and Mpw1pw Models
-
Adamo, C.; Barone, V. Exchange Functionals with Improved Longrange Behavior and Adiabatic Connection Methods without Adjustable Parameters: The Mpw and Mpw1pw Models J. Chem. Phys. 1998, 108, 664-675 10.1063/1.475428
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 664-675
-
-
Adamo, C.1
Barone, V.2
-
71
-
-
0345491105
-
Development of the Colic-Salvetti Correlation-Energy Formula into a Functional of the Electron Density
-
Lee, C. T.; Yang, W. T.; Parr, R. G. Development of the Colic-Salvetti Correlation-Energy Formula into a Functional of the Electron Density Phys. Rev. B: Condens. Matter Mater. Phys. 1988, 37, 785-789 10.1103/PhysRevB.37.785
-
(1988)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.37
, pp. 785-789
-
-
Lee, C.T.1
Yang, W.T.2
Parr, R.G.3
-
72
-
-
0000189651
-
Density-functional Thermochemistry. III. the Role of Exact Exchange
-
Becke, A. D. Density-functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652 10.1063/1.464913
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
73
-
-
34250817103
-
A New Mixing of Hartree-Fock and Local Density-Functional Theories
-
Becke, A. D. A New Mixing of Hartree-Fock and Local Density-Functional Theories J. Chem. Phys. 1993, 98, 1372-1377 10.1063/1.464304
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 1372-1377
-
-
Becke, A.D.1
-
74
-
-
22744441344
-
Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions
-
Zhao, Y.; Truhlar, D. G. Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions J. Phys. Chem. A 2005, 109, 5656-5667 10.1021/jp050536c
-
(2005)
J. Phys. Chem. A
, vol.109
, pp. 5656-5667
-
-
Zhao, Y.1
Truhlar, D.G.2
-
75
-
-
33847207462
-
Density Functional Theory with Dispersion Corrections for Supramolecular Structures, Aggregates, and Complexes of (Bio)Organic Molecules
-
Grimme, S.; Antony, J.; Schwabe, T.; Mück-Lichtenfeld, C. Density Functional Theory with Dispersion Corrections for Supramolecular Structures, Aggregates, and Complexes of (Bio)Organic Molecules Org. Biomol. Chem. 2007, 5, 741-758 10.1039/B615319B
-
(2007)
Org. Biomol. Chem.
, vol.5
, pp. 741-758
-
-
Grimme, S.1
Antony, J.2
Schwabe, T.3
Mück-Lichtenfeld, C.4
-
76
-
-
84875674943
-
Density Functional Theory with London Dispersion Corrections
-
Grimme, S. Density Functional Theory with London Dispersion Corrections WIREs Comput. Mol. Sci. 2011, 1, 211-228 10.1002/wcms.30
-
(2011)
WIREs Comput. Mol. Sci.
, vol.1
, pp. 211-228
-
-
Grimme, S.1
-
77
-
-
33750559983
-
Semiempirical GGA-type Density-Functional Constructed with A Long-Range Dispersion Correction
-
Grimme, S. Semiempirical GGA-type Density-Functional Constructed with A Long-Range Dispersion Correction J. Comput. Chem. 2006, 27, 1787-1799 10.1002/jcc.20495
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1787-1799
-
-
Grimme, S.1
-
78
-
-
77951680464
-
A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu
-
Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
-
(2010)
J. Chem. Phys.
, vol.132
, pp. 154104
-
-
Grimme, S.1
Antony, J.2
Ehrlich, S.3
Krieg, H.4
-
79
-
-
79952943559
-
Effect of the Damping Function in Dispersion Corrected Density Functional Theory
-
Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory J. Comput. Chem. 2011, 32, 1456-1465 10.1002/jcc.21759
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1456-1465
-
-
Grimme, S.1
Ehrlich, S.2
Goerigk, L.3
-
80
-
-
84874817224
-
Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes
-
Risthaus, T.; Grimme, S. Benchmarking of London Dispersion-Accounting Density Functional Theory Methods on Very Large Molecular Complexes J. Chem. Theory Comput. 2013, 9, 1580-1591 10.1021/ct301081n
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 1580-1591
-
-
Risthaus, T.1
Grimme, S.2
-
81
-
-
79952079266
-
Density-functional Approaches to Noncovalent Interactions: A Comparison of Dispersion Corrections (DFT-D), Exchange-Hole Dipole Moment (XDM) Theory, and Specialized Functionals
-
Burns, L. A.; Vázquez-Mayagoitia, A.; Sumpter, B. G.; Sherrill, C. D. Density-functional Approaches to Noncovalent Interactions: A Comparison of Dispersion Corrections (DFT-D), Exchange-Hole Dipole Moment (XDM) Theory, and Specialized Functionals J. Chem. Phys. 2011, 134, 084107 10.1063/1.3545971
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 084107
-
-
Burns, L.A.1
Vázquez-Mayagoitia, A.2
Sumpter, B.G.3
Sherrill, C.D.4
-
82
-
-
84941088431
-
Predicting Energetics of Supramolecular Systems Using the XDM Dispersion Model
-
Otero-de-la-Roza, A.; Johnson, E. R. Predicting Energetics of Supramolecular Systems Using the XDM Dispersion Model J. Chem. Theory Comput. 2015, 11, 4033-4040 10.1021/acs.jctc.5b00044
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 4033-4040
-
-
Otero-De-La-Roza, A.1
Johnson, E.R.2
-
83
-
-
0001257583
-
Construction of Tight-Binding-Like Potentials on the Basis of Density-Functional Theory: Application to Carbon
-
Porezag, D.; Frauenheim, T.; Köhler, T.; Seifert, G.; Kaschner, R. Construction of Tight-Binding-Like Potentials on the Basis of Density-Functional Theory: Application to Carbon Phys. Rev. B: Condens. Matter Mater. Phys. 1995, 51, 12947-12957 10.1103/PhysRevB.51.12947
-
(1995)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.51
, pp. 12947-12957
-
-
Porezag, D.1
Frauenheim, T.2
Köhler, T.3
Seifert, G.4
Kaschner, R.5
-
84
-
-
1542779956
-
Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties
-
Elstner, M.; Porezag, D.; Jungnickel, G.; Elsner, J.; Haugk, M.; Frauenheim, T.; Suhai, S.; Seifert, G. Self-Consistent-Charge Density-Functional Tight-Binding Method for Simulations of Complex Materials Properties Phys. Rev. B: Condens. Matter Mater. Phys. 1998, 58, 7260-7268 10.1103/PhysRevB.58.7260
-
(1998)
Phys. Rev. B: Condens. Matter Mater. Phys.
, vol.58
, pp. 7260-7268
-
-
Elstner, M.1
Porezag, D.2
Jungnickel, G.3
Elsner, J.4
Haugk, M.5
Frauenheim, T.6
Suhai, S.7
Seifert, G.8
-
85
-
-
79954547473
-
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
-
Gaus, M.; Cui, Q.; Elstner, M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) J. Chem. Theory Comput. 2011, 7, 931-948 10.1021/ct100684s
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 931-948
-
-
Gaus, M.1
Cui, Q.2
Elstner, M.3
-
86
-
-
0035932162
-
Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs: A Density-Functional-Theory Based Treatment
-
Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs: A Density-Functional-Theory Based Treatment J. Chem. Phys. 2001, 114, 5149 10.1063/1.1329889
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 5149
-
-
Elstner, M.1
Hobza, P.2
Frauenheim, T.3
Suhai, S.4
Kaxiras, E.5
-
87
-
-
84918842958
-
Low-Cost Quantum Chemical Methods for Noncovalent Interactions
-
Brandenburg, J. G.; Hochheim, M.; Bredow, T.; Grimme, S. Low-Cost Quantum Chemical Methods for Noncovalent Interactions J. Phys. Chem. Lett. 2014, 5, 4275-4284 10.1021/jz5021313
-
(2014)
J. Phys. Chem. Lett.
, vol.5
, pp. 4275-4284
-
-
Brandenburg, J.G.1
Hochheim, M.2
Bredow, T.3
Grimme, S.4
-
88
-
-
0347170005
-
Self-Consistent Molecular Orbital Methods. 12. Further Extensions of Gaussian-type Basis Sets for use in Molecular-orbital Studies of Organic-molecules
-
Hehre, W. J.; Ditchfield, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. 12. Further Extensions of Gaussian-type Basis Sets for use in Molecular-orbital Studies of Organic-molecules J. Chem. Phys. 1972, 56, 2257 10.1063/1.1677527
-
(1972)
J. Chem. Phys.
, vol.56
, pp. 2257
-
-
Hehre, W.J.1
Ditchfield, R.2
Pople, J.A.3
-
89
-
-
26244461462
-
Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy
-
Weigend, F.; Ahlrichs, R. Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of Accuracy Phys. Chem. Chem. Phys. 2005, 7, 3297-3305 10.1039/b508541a
-
(2005)
Phys. Chem. Chem. Phys.
, vol.7
, pp. 3297-3305
-
-
Weigend, F.1
Ahlrichs, R.2
-
90
-
-
4143095330
-
Electron Affinities of the First-Row Atoms Revisited. Systematic Basis Sets and Wave Functions
-
Kendall, R. A.; Dunning, T. H.; Harrison, R. J. Electron Affinities of the First-Row Atoms Revisited. Systematic Basis Sets and Wave Functions J. Chem. Phys. 1992, 96, 6796-6806 10.1063/1.462569
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 6796-6806
-
-
Kendall, R.A.1
Dunning, T.H.2
Harrison, R.J.3
-
91
-
-
26844534384
-
Self-Consistent Molecular Orbital Methods. 20. A Basis Set for Correlated Wave Functions
-
Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-Consistent Molecular Orbital Methods. 20. A Basis Set for Correlated Wave Functions J. Chem. Phys. 1980, 72, 650-654 10.1063/1.438955
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 650-654
-
-
Krishnan, R.1
Binkley, J.S.2
Seeger, R.3
Pople, J.A.4
-
92
-
-
79955703065
-
Property-Optimized Gaussian Basis Sets for Molecular Response Calculations
-
Rappoport, D.; Furche, F. Property-Optimized Gaussian Basis Sets for Molecular Response Calculations J. Chem. Phys. 2010, 133, 134105 10.1063/1.3484283
-
(2010)
J. Chem. Phys.
, vol.133
, pp. 134105
-
-
Rappoport, D.1
Furche, F.2
-
93
-
-
84890021933
-
The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors
-
Boys, S. F.; Bernardi, F. The Calculation of Small Molecular Interactions by the Differences of Separate Total Energies. Some Procedures with Reduced Errors Mol. Phys. 1970, 19, 553-566 10.1080/00268977000101561
-
(1970)
Mol. Phys.
, vol.19
, pp. 553-566
-
-
Boys, S.F.1
Bernardi, F.2
-
94
-
-
0000098578
-
Basis Set Convergence of the Interaction Energy of Hydrogen-Bonded Complexes
-
Halkier, A.; Klopper, W.; Helgaker, T.; Jørgensen, P.; Taylor, P. R. Basis Set Convergence of the Interaction Energy of Hydrogen-Bonded Complexes J. Chem. Phys. 1999, 111, 9157-9167 10.1063/1.479830
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 9157-9167
-
-
Halkier, A.1
Klopper, W.2
Helgaker, T.3
Jørgensen, P.4
Taylor, P.R.5
-
95
-
-
0000038576
-
A Theoretical Investigation of the Nature of the pi-H interaction in ethene-H2O, benzene-H2O, and benzene-(H2O)(2)
-
Tarakeshwar, P.; Choi, H. S.; Lee, S. J.; Lee, J. Y.; Kim, K. S.; Ha, T.-K.; Jang, J. H.; Lee, J. G.; Lee, H. A Theoretical Investigation of the Nature of the pi-H interaction in ethene-H2O, benzene-H2O, and benzene-(H2O)(2) J. Chem. Phys. 1999, 111, 5838-5850 10.1063/1.479879
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 5838-5850
-
-
Tarakeshwar, P.1
Choi, H.S.2
Lee, S.J.3
Lee, J.Y.4
Kim, K.S.5
Ha, T.-K.6
Jang, J.H.7
Lee, J.G.8
Lee, H.9
-
96
-
-
0034317690
-
Molecular Clusters of pi-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies
-
Kim, K. S.; Tarakeshwar, P.; Lee, J. Y. Molecular Clusters of pi-Systems: Theoretical Studies of Structures, Spectra, and Origin of Interaction Energies Chem. Rev. 2000, 100, 4145-4186 10.1021/cr990051i
-
(2000)
Chem. Rev.
, vol.100
, pp. 4145-4186
-
-
Kim, K.S.1
Tarakeshwar, P.2
Lee, J.Y.3
-
97
-
-
0037129514
-
Ab Initio Study on the (OCS)2·CO2 van der Waals Trimers
-
Valdés, H.; Sordo, J. A. Ab Initio Study on the (OCS)2·CO2 van der Waals Trimers J. Phys. Chem. A 2002, 106, 3690-3701 10.1021/jp0128168
-
(2002)
J. Phys. Chem. A
, vol.106
, pp. 3690-3701
-
-
Valdés, H.1
Sordo, J.A.2
-
98
-
-
80054712743
-
Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods
-
Antony, J.; Grimme, S.; Liakos, D. G.; Neese, F. Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods J. Phys. Chem. A 2011, 115, 11210-11220 10.1021/jp203963f
-
(2011)
J. Phys. Chem. A
, vol.115
, pp. 11210-11220
-
-
Antony, J.1
Grimme, S.2
Liakos, D.G.3
Neese, F.4
-
99
-
-
84855510074
-
A DFT-D Evaluation of the Complexation of a Molecular Tweezer with Small Aromatic Molecules
-
Graton, J.; Le Questel, J.-Y.; Legouin, B.; Uriac, P.; Van de Weghe, P.; Jacquemin, D. A DFT-D Evaluation of the Complexation of a Molecular Tweezer with Small Aromatic Molecules Chem. Phys. Lett. 2012, 522, 11-16 10.1016/j.cplett.2011.11.076
-
(2012)
Chem. Phys. Lett.
, vol.522
, pp. 11-16
-
-
Graton, J.1
Le Questel, J.-Y.2
Legouin, B.3
Uriac, P.4
Van De Weghe, P.5
Jacquemin, D.6
-
100
-
-
0001260286
-
Local Treatment of Electron Correlation in Coupled Cluster Theory
-
Hampel, C.; Werner, H.-J. Local Treatment of Electron Correlation in Coupled Cluster Theory J. Chem. Phys. 1996, 104, 6286-6295 10.1063/1.471289
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 6286-6295
-
-
Hampel, C.1
Werner, H.-J.2
-
101
-
-
80055008055
-
An Efficient Local Coupled Cluster Method for Accurate Thermochemistry of Large Systems
-
Werner, H.-J.; Schütz, M. An Efficient Local Coupled Cluster Method for Accurate Thermochemistry of Large Systems J. Chem. Phys. 2011, 135, 144116 10.1063/1.3641642
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 144116
-
-
Werner, H.-J.1
Schütz, M.2
-
102
-
-
84903362650
-
Natural Triple Excitations in Local Coupled Cluster Calculations with Pair Natural Orbitals
-
Riplinger, C.; Sandhoefer, B.; Hansen, A.; Neese, F. Natural Triple Excitations in Local Coupled Cluster Calculations with Pair Natural Orbitals J. Chem. Phys. 2013, 139, 134101 10.1063/1.4821834
-
(2013)
J. Chem. Phys.
, vol.139
, pp. 134101
-
-
Riplinger, C.1
Sandhoefer, B.2
Hansen, A.3
Neese, F.4
-
103
-
-
34548243709
-
Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method
-
Fedorov, D. G.; Kitaura, K. Extending the Power of Quantum Chemistry to Large Systems with the Fragment Molecular Orbital Method J. Phys. Chem. A 2007, 111, 6904-6914 10.1021/jp0716740
-
(2007)
J. Phys. Chem. A
, vol.111
, pp. 6904-6914
-
-
Fedorov, D.G.1
Kitaura, K.2
-
104
-
-
84861168753
-
Exploring Chemistry with the Fragment Molecular Orbital Method
-
Fedorov, D. G.; Nagata, T.; Kitaura, K. Exploring Chemistry with the Fragment Molecular Orbital Method Phys. Chem. Chem. Phys. 2012, 14, 7562-7577 10.1039/c2cp23784a
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 7562-7577
-
-
Fedorov, D.G.1
Nagata, T.2
Kitaura, K.3
-
105
-
-
33646565044
-
The Polarizable Continuum Model (PCM) Interfaced with the Fragment Molecular Orbital Method (FMO)
-
Fedorov, D. G.; Kitaura, K.; Li, H.; Jensen, J. H.; Gordon, M. S. The Polarizable Continuum Model (PCM) Interfaced with the Fragment Molecular Orbital Method (FMO) J. Comput. Chem. 2006, 27, 976-985 10.1002/jcc.20406
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 976-985
-
-
Fedorov, D.G.1
Kitaura, K.2
Li, H.3
Jensen, J.H.4
Gordon, M.S.5
-
106
-
-
78649965861
-
Incorporation of Solvation Effects into the Fragment Molecular Orbital Calculations with the Poisson-Boltzmann Equation
-
Watanabe, H.; Okiyama, Y.; Nakano, T.; Tanaka, S. Incorporation of Solvation Effects Into the Fragment Molecular Orbital Calculations with the Poisson-Boltzmann Equation Chem. Phys. Lett. 2010, 500, 116-119 10.1016/j.cplett.2010.10.017
-
(2010)
Chem. Phys. Lett.
, vol.500
, pp. 116-119
-
-
Watanabe, H.1
Okiyama, Y.2
Nakano, T.3
Tanaka, S.4
-
107
-
-
67650733858
-
A Combined Effective Fragment Potential-fragment Molecular Orbital Method. I. the Energy Expression and Initial Applications
-
Nagata, T.; Fedorov, D. G.; Kitaura, K.; Gordon, M. S. A Combined Effective Fragment Potential-fragment Molecular Orbital Method. I. The Energy Expression and Initial Applications J. Chem. Phys. 2009, 131, 024101 10.1063/1.3156313
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 024101
-
-
Nagata, T.1
Fedorov, D.G.2
Kitaura, K.3
Gordon, M.S.4
-
108
-
-
38049162158
-
Accuracy of Typical Approximations in Classical Models of Intermolecular Polarization
-
Söderhjelm, P.; Öhrn, A.; Ryde, U.; Karlström, G. Accuracy of Typical Approximations in Classical Models of Intermolecular Polarization J. Chem. Phys. 2008, 128, 014102 10.1063/1.2814240
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 014102
-
-
Söderhjelm, P.1
Öhrn, A.2
Ryde, U.3
Karlström, G.4
-
109
-
-
0041377620
-
Molecular Fractionation with Conjugate Caps for Full Quantum Mechanical Calculation of Protein-Molecule Interaction Energy
-
Zhang, D. W.; Zhang, J. Z. H. Molecular Fractionation with Conjugate Caps for Full Quantum Mechanical Calculation of Protein-Molecule Interaction Energy J. Chem. Phys. 2003, 119, 3599-3605 10.1063/1.1591727
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 3599-3605
-
-
Zhang, D.W.1
Zhang, J.Z.H.2
-
110
-
-
34248152064
-
Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters
-
Dahlke, E. E.; Truhlar, D. G. Electrostatically Embedded Many-Body Expansion for Large Systems, with Applications to Water Clusters J. Chem. Theory Comput. 2007, 3, 46-53 10.1021/ct600253j
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 46-53
-
-
Dahlke, E.E.1
Truhlar, D.G.2
-
111
-
-
84918536950
-
Fragment Quantum Mechanical Calculation of Proteins and Its Applications
-
He, X.; Zhu, T.; Wang, X.; Liu, J.; Zhang, J. Z. H. Fragment Quantum Mechanical Calculation of Proteins and Its Applications Acc. Chem. Res. 2014, 47, 2748-2757 10.1021/ar500077t
-
(2014)
Acc. Chem. Res.
, vol.47
, pp. 2748-2757
-
-
He, X.1
Zhu, T.2
Wang, X.3
Liu, J.4
Zhang, J.Z.H.5
-
112
-
-
60549094599
-
How Accurate Can A Force Field Become? - A Polarizable Multipole Model Combined with Fragment-Wise Quantum-Mechanical Calculations
-
Söderhjelm, P.; Ryde, U. How Accurate Can A Force Field Become?-A Polarizable Multipole Model Combined with Fragment-Wise Quantum-Mechanical Calculations J. Phys. Chem. A 2009, 113, 617-627 10.1021/jp8073514
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 617-627
-
-
Söderhjelm, P.1
Ryde, U.2
-
113
-
-
77955916844
-
Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods
-
Steinmann, C.; Fedorov, D. G.; Jensen, J. H. Effective Fragment Molecular Orbital Method: A Merger of the Effective Fragment Potential and Fragment Molecular Orbital Methods J. Phys. Chem. A 2010, 114, 8705-8712 10.1021/jp101498m
-
(2010)
J. Phys. Chem. A
, vol.114
, pp. 8705-8712
-
-
Steinmann, C.1
Fedorov, D.G.2
Jensen, J.H.3
-
114
-
-
64249130695
-
Linear-Scaling Methods in Quantum Chemistry
-
Lipkowitz, K. B. Cundari, T. L. VCH Publishers: New York
-
Ochsenfeld, C.; Kussmann, J.; Lambrecht, D. S. Linear-Scaling Methods in Quantum Chemistry. In Reviews in Computational Chemistry; Lipkowitz, K. B.; Cundari, T. L., Eds.; VCH Publishers: New York, 2007; Vol. 23, pp 1-82.
-
(2007)
Reviews in Computational Chemistry
, vol.23
, pp. 1-82
-
-
Ochsenfeld, C.1
Kussmann, J.2
Lambrecht, D.S.3
-
115
-
-
0011621942
-
Direct Calculation of Electron Density in Density-Functional Theory
-
Yang, W. Direct Calculation of Electron Density in Density-Functional Theory Phys. Rev. Lett. 1991, 66, 1438-1441 10.1103/PhysRevLett.66.1438
-
(1991)
Phys. Rev. Lett.
, vol.66
, pp. 1438-1441
-
-
Yang, W.1
-
116
-
-
70449529413
-
Molecular Modeling and Dynamics Studies with Explicit Inclusion of Electronic Polarizability: Theory and Applications
-
Lopes, P. E. M; Roux, B.; MacKerell, A. D. Molecular Modeling and Dynamics Studies with Explicit Inclusion of Electronic Polarizability: Theory and Applications Theor. Chem. Acc. 2009, 124, 11-28 10.1007/s00214-009-0617-x
-
(2009)
Theor. Chem. Acc.
, vol.124
, pp. 11-28
-
-
Lopes, P.E.M.1
Roux, B.2
MacKerell, A.D.3
-
117
-
-
36649010414
-
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy
-
Gresh, N.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy J. Chem. Theory Comput. 2007, 3, 1960-1986 10.1021/ct700134r
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1960-1986
-
-
Gresh, N.1
Cisneros, G.A.2
Darden, T.A.3
Piquemal, J.-P.4
-
118
-
-
34548786766
-
The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions
-
Gordon, M. S.; Slipchenko, L. V.; Li, H.; Jensen, J. H. The Effective Fragment Potential: A General Method for Predicting Intermolecular Interactions Annu. Rep. Comput. Chem. 2007, 3, 177-193 10.1016/S1574-1400(07)03010-1
-
(2007)
Annu. Rep. Comput. Chem.
, vol.3
, pp. 177-193
-
-
Gordon, M.S.1
Slipchenko, L.V.2
Li, H.3
Jensen, J.H.4
-
119
-
-
0034316197
-
Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations
-
Engkvist, O.; Åstrand, P.-O.; Karlström, G. Accurate Intermolecular Potentials Obtained from Molecular Wave Functions: Bridging the Gap between Quantum Chemistry and Molecular Simulations Chem. Rev. 2000, 100, 4087-4108 10.1021/cr9900477
-
(2000)
Chem. Rev.
, vol.100
, pp. 4087-4108
-
-
Engkvist, O.1
Åstrand, P.-O.2
Karlström, G.3
-
120
-
-
70350402094
-
A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the {Qm} Region for Peptidic Systems
-
Sumowski; Ochsenfeld A Convergence Study of QM/MM Isomerization Energies with the Selected Size of the {Qm} Region for Peptidic Systems J. Phys. Chem. A 2009, 113, 11734-11741 10.1021/jp902876n
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 11734-11741
-
-
Sumowski1
Ochsenfeld2
-
121
-
-
70350432531
-
Do Quantum Mechanical Energies Calculated for Small Models of Protein Active Sites Converge?
-
Hu, L.; Eliasson, J.; Heimdal, J.; Ryde, U. Do Quantum Mechanical Energies Calculated for Small Models of Protein Active Sites Converge? J. Phys. Chem. A 2009, 113, 11793-11800 10.1021/jp9029024
-
(2009)
J. Phys. Chem. A
, vol.113
, pp. 11793-11800
-
-
Hu, L.1
Eliasson, J.2
Heimdal, J.3
Ryde, U.4
-
122
-
-
84884185644
-
Effect of Geometry Optimisations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins
-
Sumner, S.; Söderhjelm, P.; Ryde, U. Effect of Geometry Optimisations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins J. Chem. Theory Comput. 2013, 9, 4205-4214 10.1021/ct400339c
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 4205-4214
-
-
Sumner, S.1
Söderhjelm, P.2
Ryde, U.3
-
123
-
-
84876495122
-
On the Effect of Varying Constraints in the Quantum Mechanics only Modeling of Enzymatic Reactions: The Case of Acetylene Hydratase
-
Liao, R.-Z.; Thiel, W. On the Effect of Varying Constraints in the Quantum Mechanics Only Modeling of Enzymatic Reactions: The Case of Acetylene Hydratase J. Phys. Chem. B 2013, 117, 3954-3961 10.1021/jp311705s
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 3954-3961
-
-
Liao, R.-Z.1
Thiel, W.2
-
124
-
-
31144441067
-
2 + H2 Oxidative Addition
-
2 + H2 Oxidative Addition J. Phys. Chem. 1996, 100, 19357-19363 10.1021/jp962071j
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 19357-19363
-
-
Svensson, M.1
Humbel, S.2
Froese, R.D.J.3
Matsubara, T.4
Sieber, S.5
Morokuma, K.6
-
125
-
-
79952607247
-
On the convergence of QM/MM energies
-
Hu, L.; Söderhjelm, P.; Ryde, U. On the convergence of QM/MM energies J. Chem. Theory Comput. 2011, 7, 761-777 10.1021/ct100530r
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 761-777
-
-
Hu, L.1
Söderhjelm, P.2
Ryde, U.3
-
126
-
-
0035828026
-
The Combined Multiconfigurational Self-Consistent-Field Molecular Mechanics Wave Function Approach
-
Poulsen, T. D.; Kongsted, J.; Osted, A.; Ogilby, P. R.; Mikkelsen, K. V. The Combined Multiconfigurational Self-Consistent-Field Molecular Mechanics Wave Function Approach J. Chem. Phys. 2001, 115, 2393-2400 10.1063/1.1374559
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 2393-2400
-
-
Poulsen, T.D.1
Kongsted, J.2
Osted, A.3
Ogilby, P.R.4
Mikkelsen, K.V.5
-
127
-
-
65349179259
-
Protein Influence on Electronic Spectra Modelled by Multipoles and Polarisabilities
-
Söderhjelm, P.; Husberg, C.; Strambi, A.; Olivucci, M.; Ryde, U. Protein Influence on Electronic Spectra Modelled by Multipoles and Polarisabilities J. Chem. Theory Comput. 2009, 5, 649-658 10.1021/ct800459t
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 649-658
-
-
Söderhjelm, P.1
Husberg, C.2
Strambi, A.3
Olivucci, M.4
Ryde, U.5
-
128
-
-
60749119131
-
Development and Application of Ab Initio QM/MM Methods for Mechanistic Simulation of Reactions in Solution and in Enzymes
-
Hu, H.; Yang, W. Development and Application of Ab Initio QM/MM Methods for Mechanistic Simulation of Reactions in Solution and in Enzymes J. Mol. Struct.: THEOCHEM 2009, 898, 17-30 10.1016/j.theochem.2008.12.025
-
(2009)
J. Mol. Struct.: THEOCHEM
, vol.898
, pp. 17-30
-
-
Hu, H.1
Yang, W.2
-
129
-
-
85051912728
-
Quantum Mechanical Free Energy Barrier for an Enzymatic Reaction
-
Rod, T. H.; Ryde, U. Quantum Mechanical Free Energy Barrier for an Enzymatic Reaction Phys. Rev. Lett. 2005, 94, 138302 10.1103/PhysRevLett.94.138302
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 138302
-
-
Rod, T.H.1
Ryde, U.2
-
130
-
-
84872130995
-
Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations
-
Hu, L.; Söderhjelm, P.; Ryde, U. Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations J. Chem. Theory Comput. 2013, 9, 640-649 10.1021/ct3005003
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 640-649
-
-
Hu, L.1
Söderhjelm, P.2
Ryde, U.3
-
131
-
-
84884907008
-
Convergence in the QM-Only and QM/MM Modeling of Enzymatic Reactions: A Case Study for Acetylene Hydratase
-
Liao, R.-Z.; Thiel, W. Convergence in the QM-Only and QM/MM Modeling of Enzymatic Reactions: A Case Study for Acetylene Hydratase J. Comput. Chem. 2013, 34, 2389-2397 10.1002/jcc.23403
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2389-2397
-
-
Liao, R.-Z.1
Thiel, W.2
-
132
-
-
84961980477
-
Quantum Mechanical Continuum Solvation Models
-
Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models Chem. Rev. 2005, 105, 2999-3094 10.1021/cr9904009
-
(2005)
Chem. Rev.
, vol.105
, pp. 2999-3094
-
-
Tomasi, J.1
Mennucci, B.2
Cammi, R.3
-
133
-
-
84981583952
-
Analytical Experssions of the Free-energy Derivatives for Molecules in Solution - Application to the Geometry Optimization
-
Cossi, M.; Tomasi, J.; Cammi, R. Analytical Experssions of the Free-energy Derivatives for Molecules in Solution-Application to the Geometry Optimization Int. J. Quantum Chem. 1995, 56, 695-702 10.1002/qua.560560876
-
(1995)
Int. J. Quantum Chem.
, vol.56
, pp. 695-702
-
-
Cossi, M.1
Tomasi, J.2
Cammi, R.3
-
134
-
-
84946893847
-
Electrostatic Interaction of a Solute with a Continuum. A Direct Utilization of Ab initio Molecular Potentials for the Prevision of Solvent Effects
-
Miertus, S.; Scrocco, E.; Tomasi, J. Electrostatic Interaction of a Solute with a Continuum. A Direct Utilization of Ab initio Molecular Potentials for the Prevision of Solvent Effects Chem. Phys. 1981, 55, 117-129 10.1016/0301-0104(81)85090-2
-
(1981)
Chem. Phys.
, vol.55
, pp. 117-129
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
135
-
-
84961980743
-
COSMO: A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient
-
Klamt, A.; Schüürmann, G. COSMO: a New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient J. Chem. Soc., Perkin Trans. 2 1993, 799-805 10.1039/P29930000799
-
(1993)
J. Chem. Soc., Perkin Trans. 2
, pp. 799-805
-
-
Klamt, A.1
Schüürmann, G.2
-
136
-
-
84982317161
-
The Generalized Born Approach
-
Hoijtink, G. J.; de Boer, E.; Van der Meij, P. H.; Weijland, E. P. The Generalized Born Approach Recl Trav Pays-Bas 1956, 75, 487-503 10.1002/recl.19560750502
-
(1956)
Recl Trav Pays-Bas
, vol.75
, pp. 487-503
-
-
Hoijtink, G.J.1
De Boer, E.2
Van Der Meij, P.H.3
Weijland, E.P.4
-
137
-
-
0344778061
-
Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics
-
Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics J. Am. Chem. Soc. 1990, 112, 6127-6129 10.1021/ja00172a038
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
138
-
-
0020475509
-
Calculation of the Electric Potential in the Active Site Cleft Due to α-Helix Dipoles
-
Warwicker, J.; Watson, H. C. Calculation of the Electric Potential in the Active Site Cleft Due to α-Helix Dipoles J. Mol. Biol. 1982, 157, 671-679 10.1016/0022-2836(82)90505-8
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 671-679
-
-
Warwicker, J.1
Watson, H.C.2
-
139
-
-
0029157053
-
Salt Effects on Nucleic Acids
-
Sharp, K. A.; Honig, B. Salt Effects on Nucleic Acids Curr. Opin. Struct. Biol. 1995, 5, 323-328 10.1016/0959-440X(95)80093-X
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 323-328
-
-
Sharp, K.A.1
Honig, B.2
-
140
-
-
84988074929
-
Evaluation of the Dispersion Contribution to the Solvation Energy. A Simple Computational Model in the Continuum Approximation
-
Floris, F.; Tomasi, J. Evaluation of the Dispersion Contribution to the Solvation Energy. A Simple Computational Model in the Continuum Approximation J. Comput. Chem. 1989, 10, 616-627 10.1002/jcc.540100504
-
(1989)
J. Comput. Chem.
, vol.10
, pp. 616-627
-
-
Floris, F.1
Tomasi, J.2
-
141
-
-
84961981991
-
A New Definition of Cavities for the Computation of Solvation Free Energies by the Polarizable Continuum Model
-
Barone, V.; Cossi, M.; Tomasi, J. A New Definition of Cavities for the Computation of Solvation Free Energies by the Polarizable Continuum Model J. Chem. Phys. 1997, 107, 3210-3221 10.1063/1.474671
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 3210-3221
-
-
Barone, V.1
Cossi, M.2
Tomasi, J.3
-
142
-
-
66349120487
-
Universal Solvation Model Based on Solute Electron Density and A Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions
-
Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. Universal Solvation Model Based on Solute Electron Density and A Continuum Model of the Solvent Defined by the Bulk Dielectric Constant and Atomic Surface Tensions J. Phys. Chem. B 2009, 113, 6378-6396 10.1021/jp810292n
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 6378-6396
-
-
Marenich, A.V.1
Cramer, C.J.2
Truhlar, D.G.3
-
143
-
-
33751157086
-
Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena
-
Klamt, A. Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena J. Phys. Chem. 1995, 99, 2224-2235 10.1021/j100007a062
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 2224-2235
-
-
Klamt, A.1
-
144
-
-
0036473751
-
Fast Solvent Screening via Quantum Chemistry:COSMO-RS Approach
-
Eckert, F.; Klamt, A. Fast Solvent Screening via Quantum Chemistry:COSMO-RS Approach AIChE J. 2002, 48, 369-385 10.1002/aic.690480220
-
(2002)
AIChE J.
, vol.48
, pp. 369-385
-
-
Eckert, F.1
Klamt, A.2
-
145
-
-
77955003137
-
Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories
-
Riley, K. E.; Pitonák, M.; Jurecka, P.; Hobza, P. Stabilization and Structure Calculations for Noncovalent Interactions in Extended Molecular Systems Based on Wave Function and Density Functional Theories Chem. Rev. 2010, 110, 5023-5063 10.1021/cr1000173
-
(2010)
Chem. Rev.
, vol.110
, pp. 5023-5063
-
-
Riley, K.E.1
Pitonák, M.2
Jurecka, P.3
Hobza, P.4
-
146
-
-
84859917592
-
Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies
-
Hobza, P. Calculations on Noncovalent Interactions and Databases of Benchmark Interaction Energies Acc. Chem. Res. 2012, 45, 663-672 10.1021/ar200255p
-
(2012)
Acc. Chem. Res.
, vol.45
, pp. 663-672
-
-
Hobza, P.1
-
147
-
-
84898490480
-
Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches
-
Li, A.; Muddana, H. S.; Gilson, M. K. Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches J. Chem. Theory Comput. 2014, 10, 1563-1575 10.1021/ct401111c
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1563-1575
-
-
Li, A.1
Muddana, H.S.2
Gilson, M.K.3
-
148
-
-
79952090060
-
Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-Ligand Complexes
-
Faver, J. C.; Benson, M. L.; He, X.; Roberts, B. P.; Wang, B.; Marshall, M. S.; Kennedy, M. R.; Sherrill, C. D.; Merz, K. M. Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-Ligand Complexes J. Chem. Theory Comput. 2011, 7, 790-797 10.1021/ct100563b
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 790-797
-
-
Faver, J.C.1
Benson, M.L.2
He, X.3
Roberts, B.P.4
Wang, B.5
Marshall, M.S.6
Kennedy, M.R.7
Sherrill, C.D.8
Merz, K.M.9
-
149
-
-
79955552707
-
The Energy Computation Paradox and Ab Initio Protein Folding
-
Faver, J. C.; Benson, M. L.; He, X.; Roberts, B. P.; Wang, B.; Marshall, M. S.; Sherrill, C. D.; Merz, K. M. The Energy Computation Paradox and Ab Initio Protein Folding PLoS One 2011, 6, e18868 10.1371/journal.pone.0018868
-
(2011)
PLoS One
, vol.6
, pp. e18868
-
-
Faver, J.C.1
Benson, M.L.2
He, X.3
Roberts, B.P.4
Wang, B.5
Marshall, M.S.6
Sherrill, C.D.7
Merz, K.M.8
-
150
-
-
84880163667
-
Comparison of Molecular Mechanics, Semi-Empirical Quantum Mechanical, and Density Functional Theory Methods for Scoring Protein-Ligand Interactions
-
Yilmazer, N. D.; Korth, M. Comparison of Molecular Mechanics, Semi-Empirical Quantum Mechanical, and Density Functional Theory Methods for Scoring Protein-Ligand Interactions J. Phys. Chem. B 2013, 117, 8075-8084 10.1021/jp402719k
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 8075-8084
-
-
Yilmazer, N.D.1
Korth, M.2
-
151
-
-
84928402811
-
Benchmark of Electronic Structure Methods for Protein-Ligand Interactions Based on High-Level Reference Data
-
Yilmazer, N. D.; Heitel, P.; Schwabe, T.; Korth, M. Benchmark of Electronic Structure Methods for Protein-Ligand Interactions Based on High-Level Reference Data J. Theor. Comput. Chem. 2015, 14, 1540001 10.1142/S0219633615400015
-
(2015)
J. Theor. Comput. Chem.
, vol.14
, pp. 1540001
-
-
Yilmazer, N.D.1
Heitel, P.2
Schwabe, T.3
Korth, M.4
-
152
-
-
84860116357
-
A Geometrical Correction for the Inter- and Intra-Molecular Basis Set Superposition Error in Hartree-Fock and Density Functional Theory Calculations for Large Systems
-
Kruse, H.; Grimme, S. A Geometrical Correction for the Inter- and Intra-Molecular Basis Set Superposition Error in Hartree-Fock and Density Functional Theory Calculations for Large Systems J. Chem. Phys. 2012, 136, 154101 10.1063/1.3700154
-
(2012)
J. Chem. Phys.
, vol.136
, pp. 154101
-
-
Kruse, H.1
Grimme, S.2
-
153
-
-
84870865284
-
Why the Standard B3LYP/6-31G∗ Model Chemistry should not be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem
-
Kruse, H.; Goerigk, L.; Grimme, S. Why the Standard B3LYP/6-31G∗ Model Chemistry should not be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem J. Org. Chem. 2012, 77, 10824-10834 10.1021/jo302156p
-
(2012)
J. Org. Chem.
, vol.77
, pp. 10824-10834
-
-
Kruse, H.1
Goerigk, L.2
Grimme, S.3
-
154
-
-
84879214573
-
Corrected Small Basis Set Hartree-Fock Method for Large Systems
-
Sure, R.; Grimme, S. Corrected Small Basis Set Hartree-Fock Method for Large Systems J. Comput. Chem. 2013, 34, 1672-1685 10.1002/jcc.23317
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 1672-1685
-
-
Sure, R.1
Grimme, S.2
-
155
-
-
84938793950
-
Consistent Structures and Interactions by Density Functional Theory with Small Atomic Orbital Basis Sets
-
Grimme, S.; Brandenburg, J. G.; Bannwarth, C.; Hansen, A. Consistent Structures and Interactions by Density Functional Theory with Small Atomic Orbital Basis Sets J. Chem. Phys. 2015, 143, 054107 10.1063/1.4927476
-
(2015)
J. Chem. Phys.
, vol.143
, pp. 054107
-
-
Grimme, S.1
Brandenburg, J.G.2
Bannwarth, C.3
Hansen, A.4
-
156
-
-
84862239263
-
Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model
-
Muddana, H. S.; Gilson, M. K. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model J. Chem. Theory Comput. 2012, 8, 2023-2033 10.1021/ct3002738
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2023-2033
-
-
Muddana, H.S.1
Gilson, M.K.2
-
157
-
-
84896306703
-
Bringing Clarity to the Prediction of Protein-Ligand Binding Energies Via Blurring
-
Ucisik, M. N.; Zheng, Z.; Faver, J. C.; Merz, K. M. Bringing Clarity to the Prediction of Protein-Ligand Binding Energies Via Blurring J. Chem. Theory Comput. 2014, 10, 1314-1325 10.1021/ct400995c
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1314-1325
-
-
Ucisik, M.N.1
Zheng, Z.2
Faver, J.C.3
Merz, K.M.4
-
158
-
-
0028155689
-
A New Method for Predicting Binding Affinity in Computer-Aided Drug Design
-
Åqvist, J.; Medina, C.; Samuelsson, J.-E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design Protein Eng., Des. Sel. 1994, 7, 385-391 10.1093/protein/7.3.385
-
(1994)
Protein Eng., Des. Sel.
, vol.7
, pp. 385-391
-
-
Åqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
159
-
-
0030134110
-
On the Validity of Electrostatic Linear Response in Polar Solvents
-
Åqvist, J.; Hansson, T. On the Validity of Electrostatic Linear Response in Polar Solvents J. Phys. Chem. 1996, 100, 9512-9521 10.1021/jp953640a
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 9512-9521
-
-
Åqvist, J.1
Hansson, T.2
-
160
-
-
36649023306
-
Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies
-
Almlöf, M.; Carlsson, J.; Åqvist, J. Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies J. Chem. Theory Comput. 2007, 3, 2162-2175 10.1021/ct700106b
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2162-2175
-
-
Almlöf, M.1
Carlsson, J.2
Åqvist, J.3
-
161
-
-
42949174603
-
Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-Nucleoside Inhibitors to HIV-1 Reverse Transcriptase
-
Carlsson, J.; Boukharta, L.; Åqvist, J. Combining Docking, Molecular Dynamics and the Linear Interaction Energy Method to Predict Binding Modes and Affinities for Non-Nucleoside Inhibitors to HIV-1 Reverse Transcriptase J. Med. Chem. 2008, 51, 2648-2656 10.1021/jm7012198
-
(2008)
J. Med. Chem.
, vol.51
, pp. 2648-2656
-
-
Carlsson, J.1
Boukharta, L.2
Åqvist, J.3
-
162
-
-
33845335781
-
Towards Predictive Ligand Design with Free-Energy Based Computational Methods?
-
Foloppe, N.; Hubbard, R. Towards Predictive Ligand Design with Free-Energy Based Computational Methods? Curr. Med. Chem. 2006, 13, 3583-3608 10.2174/092986706779026165
-
(2006)
Curr. Med. Chem.
, vol.13
, pp. 3583-3608
-
-
Foloppe, N.1
Hubbard, R.2
-
163
-
-
0001389474
-
An Extended Linear Response Method for Determining Free Energies of Hydration
-
Carlson, H. A.; Jorgensen, W. L. An Extended Linear Response Method for Determining Free Energies of Hydration J. Phys. Chem. 1995, 99, 10667-10673 10.1021/j100026a034
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 10667-10673
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
164
-
-
2342636434
-
General Model for Estimation of the Inhibition of Protein Kinases using Monte Carlo Simulations
-
Tominaga, Y.; Jorgensen, W. L. General Model for Estimation of the Inhibition of Protein Kinases using Monte Carlo Simulations J. Med. Chem. 2004, 47, 2534-2549 10.1021/jm0304358
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2534-2549
-
-
Tominaga, Y.1
Jorgensen, W.L.2
-
165
-
-
7444257387
-
Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation
-
Huang, D.; Caflisch, A. Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation J. Med. Chem. 2004, 47, 5791-5797 10.1021/jm049726m
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5791-5797
-
-
Huang, D.1
Caflisch, A.2
-
166
-
-
0032560959
-
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
-
Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120, 9401-9409 10.1021/ja981844+
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
167
-
-
84928313330
-
The MM/PBSA and MM/GBSA Methods to Estimate Ligand-binding Affinities
-
Genheden, S.; Ryde, U. The MM/PBSA and MM/GBSA Methods to Estimate Ligand-binding Affinities Expert Opin. Drug Discovery 2015, 10, 449-461 10.1517/17460441.2015.1032936
-
(2015)
Expert Opin. Drug Discovery
, vol.10
, pp. 449-461
-
-
Genheden, S.1
Ryde, U.2
-
168
-
-
36849122972
-
High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
-
Zwanzig, R. W. High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases J. Chem. Phys. 1954, 22, 1420-1427 10.1063/1.1740409
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420-1427
-
-
Zwanzig, R.W.1
-
169
-
-
33646471468
-
Statistical Mechanics of Fluid Mixtures
-
Kirkwood, J. G. Statistical Mechanics of Fluid Mixtures J. Chem. Phys. 1935, 3, 300-313 10.1063/1.1749657
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
170
-
-
5244304444
-
Efficient Estimation of Free Energy Differences from Monte Carlo Data
-
Bennett, C. H. Efficient Estimation of Free Energy Differences from Monte Carlo Data J. Comput. Phys. 1976, 22, 245-268 10.1016/0021-9991(76)90078-4
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
171
-
-
23944432199
-
Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration
-
Shirts, M. R.; Pande, V. S. Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration J. Chem. Phys. 2005, 122, 144107 10.1063/1.1873592
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 144107
-
-
Shirts, M.R.1
Pande, V.S.2
-
172
-
-
52949088587
-
Statistically Optimal Analysis of Samples from Multiple Equilibrium States
-
Shirts, M. R.; Chodera, J. D. Statistically Optimal Analysis of Samples From Multiple Equilibrium States J. Chem. Phys. 2008, 129, 124105 10.1063/1.2978177
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 124105
-
-
Shirts, M.R.1
Chodera, J.D.2
-
173
-
-
0141682863
-
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
-
Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute Binding Free Energies: A Quantitative Approach for Their Calculation J. Phys. Chem. B 2003, 107, 9535-9551 10.1021/jp0217839
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
174
-
-
33749238080
-
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
-
Deng, Y.; Roux, B. Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant J. Chem. Theory Comput. 2006, 2, 1255-1273 10.1021/ct060037v
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1255-1273
-
-
Deng, Y.1
Roux, B.2
-
175
-
-
0035846166
-
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
-
Pearlman, D. A.; Charifson, P. S. Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System J. Med. Chem. 2001, 44, 3417-3423 10.1021/jm0100279
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
176
-
-
84859444429
-
Binding Affinities of the SAMPL3 Trypsin and Host-Guest Blind Tests Estimated with the MM/PBSA and LIE Methods
-
Mikulskis, P.; Genheden, S.; Rydberg, P.; Sandberg, L.; Olsen, L.; Ryde, U. Binding Affinities of the SAMPL3 Trypsin and Host-Guest Blind Tests Estimated with the MM/PBSA and LIE Methods J. Comput.-Aided Mol. Des. 2012, 26, 527-541 10.1007/s10822-011-9524-z
-
(2012)
J. Comput.-Aided Mol. Des.
, vol.26
, pp. 527-541
-
-
Mikulskis, P.1
Genheden, S.2
Rydberg, P.3
Sandberg, L.4
Olsen, L.5
Ryde, U.6
-
177
-
-
76249085850
-
How to Obtain Statistically Converged MM/GBSA Results
-
Genheden, S.; Ryde, U. How to Obtain Statistically Converged MM/GBSA Results J. Comput. Chem. 2010, 31, 837-846 10.1002/jcc.21366
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 837-846
-
-
Genheden, S.1
Ryde, U.2
-
178
-
-
79955450554
-
Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation
-
Kolár, M.; Fanfrlík, J.; Hobza, P. Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation J. Phys. Chem. B 2011, 115, 4718-4724 10.1021/jp2010265
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 4718-4724
-
-
Kolár, M.1
Fanfrlík, J.2
Hobza, P.3
-
179
-
-
79952586541
-
New Ultrahigh Affinity Host-Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations
-
Moghaddam, S.; Yang, C.; Rekharsky, M.; Ko, Y. H.; Kim, K.; Inoue, Y.; Gilson, M. K. New Ultrahigh Affinity Host-Guest Complexes of Cucurbit[7]uril with Bicyclo[2.2.2]octane and Adamantane Guests: Thermodynamic Analysis and Evaluation of M2 Affinity Calculations J. Am. Chem. Soc. 2011, 133, 3570-3581 10.1021/ja109904u
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 3570-3581
-
-
Moghaddam, S.1
Yang, C.2
Rekharsky, M.3
Ko, Y.H.4
Kim, K.5
Inoue, Y.6
Gilson, M.K.7
-
180
-
-
16344395749
-
Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design
-
Chen, W.; Chang, C.-E.; Gilson, M. K. Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design Biophys. J. 2004, 87, 3035-3049 10.1529/biophysj.104.049494
-
(2004)
Biophys. J.
, vol.87
, pp. 3035-3049
-
-
Chen, W.1
Chang, C.-E.2
Gilson, M.K.3
-
181
-
-
70349100806
-
Theory of Free Energy and Entropy in Noncovalent Binding
-
Zhou, H.-X.; Gilson, M. K. Theory of Free Energy and Entropy in Noncovalent Binding Chem. Rev. 2009, 109, 4092-4107 10.1021/cr800551w
-
(2009)
Chem. Rev.
, vol.109
, pp. 4092-4107
-
-
Zhou, H.-X.1
Gilson, M.K.2
-
182
-
-
0035296992
-
Isokinetic Relationship, Isoequilibrium Relationship, and Enthalpy-Entropy Compensation
-
Liu, L.; Guo, Q.-X. Isokinetic Relationship, Isoequilibrium Relationship, and Enthalpy-Entropy Compensation Chem. Rev. 2001, 101, 673-696 10.1021/cr990416z
-
(2001)
Chem. Rev.
, vol.101
, pp. 673-696
-
-
Liu, L.1
Guo, Q.-X.2
-
183
-
-
0035107447
-
Entropy-Enthalpy Compensation: Fact or Artifact?
-
Sharp, K. Entropy-Enthalpy Compensation: Fact or Artifact? Protein Sci. 2001, 10, 661-667 10.1110/ps.37801
-
(2001)
Protein Sci.
, vol.10
, pp. 661-667
-
-
Sharp, K.1
-
184
-
-
84877768087
-
Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design
-
Chodera, J. D.; Mobley, D. L. Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design Annu. Rev. Biophys. 2013, 42, 121-142 10.1146/annurev-biophys-083012-130318
-
(2013)
Annu. Rev. Biophys.
, vol.42
, pp. 121-142
-
-
Chodera, J.D.1
Mobley, D.L.2
-
185
-
-
84906539098
-
A Fundamental View of Enthalpy-Entropy Compensation
-
Ryde, U. A Fundamental View of Enthalpy-Entropy Compensation MedChemComm 2014, 5, 1324-1336 10.1039/C4MD00057A
-
(2014)
MedChemComm
, vol.5
, pp. 1324-1336
-
-
Ryde, U.1
-
186
-
-
0036667496
-
Quantum Chemical Geometry Optimisations in Proteins Using Crystallographic Raw Data
-
Ryde, U.; Olsen, L.; Nilsson, K. Quantum Chemical Geometry Optimisations in Proteins Using Crystallographic Raw Data J. Comput. Chem. 2002, 23, 1058-1070 10.1002/jcc.10093
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1058-1070
-
-
Ryde, U.1
Olsen, L.2
Nilsson, K.3
-
187
-
-
0028569736
-
Quantum Mechanical Model Assembly Study on the Energetics of Binding of Arabinose, Fucose, and Galactose to L-Arabinose-Binding Protein
-
Peräkylä, M.; Pakkanen, T. A. Quantum Mechanical Model Assembly Study on the Energetics of Binding of Arabinose, Fucose, and Galactose to L-Arabinose-Binding Protein Proteins: Struct., Funct., Genet. 1994, 20, 367-372 10.1002/prot.340200409
-
(1994)
Proteins: Struct., Funct., Genet.
, vol.20
, pp. 367-372
-
-
Peräkylä, M.1
Pakkanen, T.A.2
-
188
-
-
0028831214
-
Model Assembly Study of the Ligand Binding by P-Hydroxybenzoate Hydroxylase: Correlation between the Calculated Binding Energies and the Experimental Dissociation Constants
-
Peräkylä, M.; Pakkanen, T. A. Model Assembly Study of the Ligand Binding by P-Hydroxybenzoate Hydroxylase: Correlation between the Calculated Binding Energies and the Experimental Dissociation Constants Proteins: Struct., Funct., Genet. 1995, 21, 22-29 10.1002/prot.340210104
-
(1995)
Proteins: Struct., Funct., Genet.
, vol.21
, pp. 22-29
-
-
Peräkylä, M.1
Pakkanen, T.A.2
-
189
-
-
1542273631
-
Semiempirical Calculations of Binding Enthalpy for Protein-Ligand Complexes
-
Nikitina, E.; Sulimov, V.; Zayets, V.; Zaitseva, N. Semiempirical Calculations of Binding Enthalpy for Protein-Ligand Complexes Int. J. Quantum Chem. 2004, 97, 747-763 10.1002/qua.10778
-
(2004)
Int. J. Quantum Chem.
, vol.97
, pp. 747-763
-
-
Nikitina, E.1
Sulimov, V.2
Zayets, V.3
Zaitseva, N.4
-
190
-
-
33646260465
-
Mixed Implicit/Explicit Solvation Models in Quantum Mechanical Calculations of Binding Enthalpy for Protein-Ligand Complexes
-
Nikitina, E.; Sulimov, V.; Grigoriev, F.; Kondakova, O.; Luschekina, S. Mixed Implicit/Explicit Solvation Models in Quantum Mechanical Calculations of Binding Enthalpy for Protein-Ligand Complexes Int. J. Quantum Chem. 2006, 106, 1943-1963 10.1002/qua.20943
-
(2006)
Int. J. Quantum Chem.
, vol.106
, pp. 1943-1963
-
-
Nikitina, E.1
Sulimov, V.2
Grigoriev, F.3
Kondakova, O.4
Luschekina, S.5
-
191
-
-
24144448070
-
Are AM1 Ligand-Protein Binding Enthalpies Good Enough for Use in the Rational Design of New Drugs?
-
Villar, R.; Gil, M. J.; García, J. I.; Martínez-Merino, V. Are AM1 Ligand-Protein Binding Enthalpies Good Enough for Use in the Rational Design of New Drugs? J. Comput. Chem. 2005, 26, 1347-1358 10.1002/jcc.20276
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1347-1358
-
-
Villar, R.1
Gil, M.J.2
García, J.I.3
Martínez-Merino, V.4
-
192
-
-
52649180981
-
Ab initio Computational Study of Positron Emission Tomography Ligands Interacting with Lipid Molecule for the Prediction of Nonspecific Binding
-
Rosso, L.; Gee, A. D.; Gould, I. R. Ab initio Computational Study of Positron Emission Tomography Ligands Interacting with Lipid Molecule for the Prediction of Nonspecific Binding J. Comput. Chem. 2008, 29, 2397-2405 10.1002/jcc.20972
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 2397-2405
-
-
Rosso, L.1
Gee, A.D.2
Gould, I.R.3
-
193
-
-
77955232886
-
Supplementing the PBSA Approach with Quantum Mechancis to Study the Binding between CDK2 and N-2-substituted O-6-Cyclohexylmethoxyguanine Inhibitors
-
Shi, J. Y.; Lu, Z. A.; Zhang, Q. L.; Wang, M. L.; Wong, C. F.; Liu, J. H. Supplementing the PBSA Approach with Quantum Mechancis to Study the Binding between CDK2 and N-2-substituted O-6-Cyclohexylmethoxyguanine Inhibitors J. Theor. Comput. Chem. 2010, 9, 543-559 10.1142/S0219633610005876
-
(2010)
J. Theor. Comput. Chem.
, vol.9
, pp. 543-559
-
-
Shi, J.Y.1
Lu, Z.A.2
Zhang, Q.L.3
Wang, M.L.4
Wong, C.F.5
Liu, J.H.6
-
194
-
-
77953213689
-
Rationalization of the Inhibition Activity of Structurally Related Organometallic Compounds against the Drug Target Cathepsin B by DFT
-
Casini, A.; Edafe, F.; Erlandsson, M.; Gonsalvi, L.; Ciancetta, A.; Re, N.; Ienco, A.; Messori, L.; Peruzzini, M.; Dyson, P. J. Rationalization of the Inhibition Activity of Structurally Related Organometallic Compounds against the Drug Target Cathepsin B by DFT Dalton Trans. 2010, 39, 5556-5563 10.1039/c003218b
-
(2010)
Dalton Trans.
, vol.39
, pp. 5556-5563
-
-
Casini, A.1
Edafe, F.2
Erlandsson, M.3
Gonsalvi, L.4
Ciancetta, A.5
Re, N.6
Ienco, A.7
Messori, L.8
Peruzzini, M.9
Dyson, P.J.10
-
195
-
-
80055066394
-
A QM/MM Study of the Binding of RAPTA Ligands to Cathepsin B
-
Ciancetta, A.; Genheden, S.; Ryde, U. A QM/MM Study of the Binding of RAPTA Ligands to Cathepsin B J. Comput.-Aided Mol. Des. 2011, 25, 729-742 10.1007/s10822-011-9448-7
-
(2011)
J. Comput.-Aided Mol. Des.
, vol.25
, pp. 729-742
-
-
Ciancetta, A.1
Genheden, S.2
Ryde, U.3
-
196
-
-
28644442414
-
Binding Energy Analysis for Wild-Type and Y181C Mutant HIV-1 RT/8-Cl TIBO Complex Structures: Quantum Chemical Calculations Based on the ONIOM Method
-
859-469
-
Saen-oon, S.; Kuno, M.; Hannongbua, S. Binding Energy Analysis for Wild-Type and Y181C Mutant HIV-1 RT/8-Cl TIBO Complex Structures: Quantum Chemical Calculations Based on the ONIOM Method Proteins: Struct., Funct., Genet. 2005, 61, 859-469 10.1002/prot.20690
-
(2005)
Proteins: Struct., Funct., Genet.
, vol.61
-
-
Saen-Oon, S.1
Kuno, M.2
Hannongbua, S.3
-
197
-
-
84872952730
-
Divide-and-Conquer-Based Quantum Chemical Study for Interaction between HIV-1 Reverse Transcriptase and MK-4965 Inhibitor
-
Saparpakorn, P.; Kobayashi, M.; Hannongbua, S.; Nakai, H. Divide-and-Conquer-Based Quantum Chemical Study for Interaction between HIV-1 Reverse Transcriptase and MK-4965 Inhibitor Int. J. Quantum Chem. 2013, 113, 510-517 10.1002/qua.24164
-
(2013)
Int. J. Quantum Chem.
, vol.113
, pp. 510-517
-
-
Saparpakorn, P.1
Kobayashi, M.2
Hannongbua, S.3
Nakai, H.4
-
198
-
-
34247897078
-
The Origins of Femtomolar Protein-Ligand Binding: Hydrogen-Bond Cooperativity and Desolvation Energetics in the Biotin-(Strept)Avidin Binding Site
-
DeChancie, J.; Houk, K. N. The Origins of Femtomolar Protein-Ligand Binding: Hydrogen-Bond Cooperativity and Desolvation Energetics in the Biotin-(Strept)Avidin Binding Site J. Am. Chem. Soc. 2007, 129, 5419-5429 10.1021/ja066950n
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 5419-5429
-
-
DeChancie, J.1
Houk, K.N.2
-
199
-
-
84902437056
-
Inhibitor Ranking through QM based Chelation Calculations for Virtual Screening of HIV-1 RNase H Inhibition
-
Poongavanam, V.; Steinmann, C.; Kongsted, J. Inhibitor Ranking through QM based Chelation Calculations for Virtual Screening of HIV-1 RNase H Inhibition PLoS One 2014, 9, e98659 10.1371/journal.pone.0098659
-
(2014)
PLoS One
, vol.9
, pp. e98659
-
-
Poongavanam, V.1
Steinmann, C.2
Kongsted, J.3
-
200
-
-
33750124980
-
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
-
Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes J. Med. Chem. 2006, 49, 6177-6196 10.1021/jm051256o
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
201
-
-
84896909024
-
Potency Prediction of ß-Secretase (BACE-1) Inhibitors Using Density-Functional Methods
-
Roos, K.; Viklund, J.; Meuller, J.; Kaspersson, K.; Svensson, M. Potency Prediction of ß-Secretase (BACE-1) Inhibitors Using Density-Functional Methods J. Chem. Inf. Model. 2014, 54, 818-825 10.1021/ci400374z
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 818-825
-
-
Roos, K.1
Viklund, J.2
Meuller, J.3
Kaspersson, K.4
Svensson, M.5
-
202
-
-
84921677485
-
Using Dispersion-Corrected Density-Functional Theory to Understand Supramolecular Binding Thermodynamics
-
Antony, J.; Sure, R.; Grimme, S. Using Dispersion-Corrected Density-Functional Theory to Understand Supramolecular Binding Thermodynamics Chem. Commun. 2015, 51, 1764-1774 10.1039/C4CC06722C
-
(2015)
Chem. Commun.
, vol.51
, pp. 1764-1774
-
-
Antony, J.1
Sure, R.2
Grimme, S.3
-
203
-
-
67849083399
-
Host-Guest Complexes with Protein-Ligand-Like Affinities: Computational Analysis and Design
-
Moghaddam, S.; Inoue, Y.; Gilson, M. K. Host-Guest Complexes with Protein-Ligand-Like Affinities: Computational Analysis and Design J. Am. Chem. Soc. 2009, 131, 4012-4021 10.1021/ja808175m
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 4012-4021
-
-
Moghaddam, S.1
Inoue, Y.2
Gilson, M.K.3
-
204
-
-
0033599295
-
···O] Interactions As A Control Element in Supramolecular Complexes: Experimental and Theoretical Evaluation of Receptor Affinities for the Binding of Bipyridinium-Based Guests by Catenated Hosts
-
···O] Interactions As A Control Element in Supramolecular Complexes: Experimental and Theoretical Evaluation of Receptor Affinities for the Binding of Bipyridinium-Based Guests by Catenated Hosts J. Am. Chem. Soc. 1999, 121, 1479-1487 10.1021/ja982748b
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 1479-1487
-
-
Houk, K.N.1
Menzer, S.2
Newton, S.P.3
Raymo, F.M.4
Stoddart, J.F.5
Williams, D.J.6
-
205
-
-
33748762575
-
A Theoretical Investigation of the Geometries and Binding Energies of Molecular Tweezer and Clip Host-Guest Systems
-
Parac, M.; Etinski, M.; Peric, M.; Grimme, S. A Theoretical Investigation of the Geometries and Binding Energies of Molecular Tweezer and Clip Host-Guest Systems J. Chem. Theory Comput. 2005, 1, 1110-1118 10.1021/ct050122n
-
(2005)
J. Chem. Theory Comput.
, vol.1
, pp. 1110-1118
-
-
Parac, M.1
Etinski, M.2
Peric, M.3
Grimme, S.4
-
206
-
-
57349095296
-
Eperimentally-Based Recommendations of Density Functionals for Predicting Properties in Mechanically Interlocked Molecules
-
Benitez, D.; Tkatchouk, E.; Yoon, I.; Stoddart, J. F.; Goddard, W. A. Eperimentally-Based Recommendations of Density Functionals for Predicting Properties in Mechanically Interlocked Molecules J. Am. Chem. Soc. 2008, 130, 14928-14929 10.1021/ja805953u
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 14928-14929
-
-
Benitez, D.1
Tkatchouk, E.2
Yoon, I.3
Stoddart, J.F.4
Goddard, W.A.5
-
207
-
-
43749094990
-
Computational Characterization and Modeling of Buckyball Tweezers: Density Functional Study of Concave-Convex π-π Interactions
-
Zhao, Y.; Truhlar, D. G. Computational Characterization and Modeling of Buckyball Tweezers: Density Functional Study of Concave-Convex π-π Interactions Phys. Chem. Chem. Phys. 2008, 10, 2813-2818 10.1039/b717744e
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2813-2818
-
-
Zhao, Y.1
Truhlar, D.G.2
-
208
-
-
84961983977
-
Does DFT-D Estimate Accurate Energies for the Binding of Ligands to Metal Complexes?
-
Ryde, U.; Mata, R. A.; Grimme, S. Does DFT-D Estimate Accurate Energies for the Binding of Ligands to Metal Complexes? Dalton Trans. 2011, 40, 11176-11183 10.1039/c1dt10867k
-
(2011)
Dalton Trans.
, vol.40
, pp. 11176-11183
-
-
Ryde, U.1
Mata, R.A.2
Grimme, S.3
-
209
-
-
84962450079
-
Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction
-
Li, J.-L.; Mata, R. A.; Ryde, U. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction J. Chem. Theory Comput. 2013, 9, 1799-1807 10.1021/ct301094r
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 1799-1807
-
-
Li, J.-L.1
Mata, R.A.2
Ryde, U.3
-
210
-
-
84864435917
-
Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory
-
Grimme, S. Supramolecular Binding Thermodynamics by Dispersion-Corrected Density Functional Theory Chem.-Eur. J. 2012, 18, 9955-9964 10.1002/chem.201200497
-
(2012)
Chem. - Eur. J.
, vol.18
, pp. 9955-9964
-
-
Grimme, S.1
-
211
-
-
84907056983
-
Intermolecular Symmetry-Adapted Perturbation Theory Study of Large Organic Complexes
-
Hesselmann, A.; Korona, T. Intermolecular Symmetry-Adapted Perturbation Theory Study of Large Organic Complexes J. Chem. Phys. 2014, 141, 094107 10.1063/1.4893990
-
(2014)
J. Chem. Phys.
, vol.141
, pp. 094107
-
-
Hesselmann, A.1
Korona, T.2
-
212
-
-
84897585985
-
Hard Numbers for Large Molecules: Toward Exact Energetics for Supramolecular Systems
-
Ambrosetti, A.; Alfe, D.; DiStasio, R. A.; Tkatchenko, A. Hard Numbers for Large Molecules: Toward Exact Energetics for Supramolecular Systems J. Phys. Chem. Lett. 2014, 5, 849-855 10.1021/jz402663k
-
(2014)
J. Phys. Chem. Lett.
, vol.5
, pp. 849-855
-
-
Ambrosetti, A.1
Alfe, D.2
DiStasio, R.A.3
Tkatchenko, A.4
-
213
-
-
84938912898
-
Comprehensive Benchmark of Association (Free) Energies of Realistic Host-Guest Complexes
-
Sure, R.; Grimme, S. Comprehensive Benchmark of Association (Free) Energies of Realistic Host-Guest Complexes J. Chem. Theory Comput. 2015, 11, 3785-3801 10.1021/acs.jctc.5b00296
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 3785-3801
-
-
Sure, R.1
Grimme, S.2
-
214
-
-
84897128453
-
Blind Prediction of Binding Affinities for Charged Supramolecular Host-Guest Systems: Achievements and Shortcomings of DFT-D3
-
Sure, R.; Antony, J.; Grimme, S. Blind Prediction of Binding Affinities for Charged Supramolecular Host-Guest Systems: Achievements and Shortcomings of DFT-D3 J. Phys. Chem. B 2014, 118, 3431-3440 10.1021/jp411616b
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 3431-3440
-
-
Sure, R.1
Antony, J.2
Grimme, S.3
-
215
-
-
84899970839
-
The SAMPL4 Host-Guest Blind Prediction Challenge: An Overview
-
Muddana, H. S.; Fenley, A. T.; Mobley, D. L.; Gilson, M. K. The SAMPL4 Host-Guest Blind Prediction Challenge: An Overview J. Comput.-Aided Mol. Des. 2014, 28, 305-317 10.1007/s10822-014-9735-1
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 305-317
-
-
Muddana, H.S.1
Fenley, A.T.2
Mobley, D.L.3
Gilson, M.K.4
-
216
-
-
84902805310
-
Free-Energy Perturbation and Quantum Mechanical Study of SAMPL4 Octa-Acid Host-Guest Binding Energies
-
Mikulskis, P.; Cioloboc, D.; Andrejic, M.; Khare, S.; Brorsson, J.; Genheden, S.; Mata, R. A.; Söderhjelm, P.; Ryde, U. Free-Energy Perturbation and Quantum Mechanical Study of SAMPL4 Octa-Acid Host-Guest Binding Energies J. Comput.-Aided Mol. Des. 2014, 28, 375-400 10.1007/s10822-014-9739-x
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 375-400
-
-
Mikulskis, P.1
Cioloboc, D.2
Andrejic, M.3
Khare, S.4
Brorsson, J.5
Genheden, S.6
Mata, R.A.7
Söderhjelm, P.8
Ryde, U.9
-
217
-
-
85027933850
-
The Association of Two "frustrated" Lewis Pairs by State- of-The-Art Quantum Chemical Methods
-
Bannwarth, C.; Hansen, A.; Grimme, S. The Association of Two "Frustrated" Lewis Pairs by State- of-the-Art Quantum Chemical Methods Isr. J. Chem. 2015, 55, 235-242 10.1002/ijch.201400138
-
(2015)
Isr. J. Chem.
, vol.55
, pp. 235-242
-
-
Bannwarth, C.1
Hansen, A.2
Grimme, S.3
-
218
-
-
24844471210
-
Fast and Accurate Predictions of Relative Binding Energies
-
Alex, A.; Finn, P. Fast and Accurate Predictions of Relative Binding Energies J. Mol. Struct.: THEOCHEM 1997, 398-399, 551-554 10.1016/S0166-1280(97)00031-6
-
(1997)
J. Mol. Struct.: THEOCHEM
, vol.398-399
, pp. 551-554
-
-
Alex, A.1
Finn, P.2
-
219
-
-
11144235131
-
A Combined QM/MM Approach to Protein-Ligand Interactions: Polarization Effects of the HIV-1 Protease on Selected High Affinity Inhibitors
-
Hensen, C.; Hermann, J. C.; Nam, K.; Ma, S.; Gao, J.; Höltje, H.-D. A Combined QM/MM Approach to Protein-Ligand Interactions: Polarization Effects of the HIV-1 Protease on Selected High Affinity Inhibitors J. Med. Chem. 2004, 47, 6673-6680 10.1021/jm0497343
-
(2004)
J. Med. Chem.
, vol.47
, pp. 6673-6680
-
-
Hensen, C.1
Hermann, J.C.2
Nam, K.3
Ma, S.4
Gao, J.5
Höltje, H.-D.6
-
220
-
-
70350561951
-
QM/MM Study of Epitope Peptides Binding to HLA-A∗0201: The Roles of Anchor Residues and Water
-
Li, Y.; Yang, Y.; He, P.; Yang, Q. QM/MM Study of Epitope Peptides Binding to HLA-A∗0201: The Roles of Anchor Residues and Water Chem. Biol. Drug Des. 2009, 74, 611-618 10.1111/j.1747-0285.2009.00896.x
-
(2009)
Chem. Biol. Drug Des.
, vol.74
, pp. 611-618
-
-
Li, Y.1
Yang, Y.2
He, P.3
Yang, Q.4
-
221
-
-
0041733948
-
Prediction of the Potency of Inhibitors of Adenosine Deaminase by QM/MM Calculations
-
Gleeson, M. P.; Burton, N. A.; Hillier, I. H. Prediction of the Potency of Inhibitors of Adenosine Deaminase by QM/MM Calculations Chem. Commun. 2003, 2180-2181 10.1039/B305790A
-
(2003)
Chem. Commun.
, pp. 2180-2181
-
-
Gleeson, M.P.1
Burton, N.A.2
Hillier, I.H.3
-
222
-
-
43449131192
-
A QM/MM study of Fluoroaromatic Interactions at the Binding Site of Carbonic Anhydrase II, Using A DFT Method Corrected for Dispersive Interactions
-
Morgado, C. A.; Hillier, I. H.; Burton, N. A.; McDouall, J. J. W. A QM/MM study of Fluoroaromatic Interactions at the Binding Site of Carbonic Anhydrase II, Using A DFT Method Corrected for Dispersive Interactions Phys. Chem. Chem. Phys. 2008, 10, 2706-2714 10.1039/b715514j
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2706-2714
-
-
Morgado, C.A.1
Hillier, I.H.2
Burton, N.A.3
McDouall, J.J.W.4
-
223
-
-
67650787057
-
Electronic Structure, Binding Energy, and Solvation Structure of the Streptavidin-Biotin Supramolecular Complex: ONIOM and 3D-RISM Study
-
Li, Q.; Gusarov, S.; Evoy, S.; Kovalenko, A. Electronic Structure, Binding Energy, and Solvation Structure of the Streptavidin-Biotin Supramolecular Complex: ONIOM and 3D-RISM Study J. Phys. Chem. B 2009, 113, 9958-9967 10.1021/jp902668c
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9958-9967
-
-
Li, Q.1
Gusarov, S.2
Evoy, S.3
Kovalenko, A.4
-
224
-
-
47049096991
-
Binding Energy Contributions of the Conserved Bridging Water Molecules in CDK2-Inhibitor Complexes: A Combined QM/MM Study
-
Jia, R.; Yang, L.-J.; Yang, S.-Y. Binding Energy Contributions of the Conserved Bridging Water Molecules in CDK2-Inhibitor Complexes: A Combined QM/MM Study Chem. Phys. Lett. 2008, 460, 300-305 10.1016/j.cplett.2008.06.002
-
(2008)
Chem. Phys. Lett.
, vol.460
, pp. 300-305
-
-
Jia, R.1
Yang, L.-J.2
Yang, S.-Y.3
-
225
-
-
84903767123
-
Insights into the Structural Basis of 3,5-Diaminoindazoles As CDK2 Inhibitors: Prediction of Binding Modes and Potency by QM-MM Interaction, MESP and MD Simulation
-
Tripathi, S. K.; Singh, S. K. Insights into the Structural Basis of 3,5-Diaminoindazoles As CDK2 Inhibitors: Prediction of Binding Modes and Potency by QM-MM Interaction, MESP and MD Simulation Mol. BioSyst. 2014, 10, 2189-2201 10.1039/C4MB00077C
-
(2014)
Mol. BioSyst.
, vol.10
, pp. 2189-2201
-
-
Tripathi, S.K.1
Singh, S.K.2
-
226
-
-
84865676787
-
Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase 9 with A Series of Biphenylsulfonamides-LERE-QSAR Analysis (V)
-
Yoshida, T.; Hitaoka, S.; Mashima, A.; Sugimoto, T.; Matoba, H.; Chuman, H. Combined QM/MM (ONIOM) and QSAR Approach to the Study of Complex Formation of Matrix Metalloproteinase 9 with A Series of Biphenylsulfonamides-LERE-QSAR Analysis (V) J. Phys. Chem. B 2012, 116, 10283-10289 10.1021/jp305476x
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 10283-10289
-
-
Yoshida, T.1
Hitaoka, S.2
Mashima, A.3
Sugimoto, T.4
Matoba, H.5
Chuman, H.6
-
227
-
-
70350515927
-
Fluorine Bonding. How Does It Work in Protein-Ligand Interactions?
-
Zhou, P.; Zou, J.; Tian, F.; Shang, Z. Fluorine Bonding. How Does It Work in Protein-Ligand Interactions? J. Chem. Inf. Model. 2009, 49, 2344-2355 10.1021/ci9002393
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2344-2355
-
-
Zhou, P.1
Zou, J.2
Tian, F.3
Shang, Z.4
-
228
-
-
18344371990
-
Insights into Saquinavir Resistance in the G48V HIV-1 Protease: Quantum Calculations and Molecular Dynamic Simulations
-
Wittayanarakul, K.; Aruksakunwong, O.; Saen-oon, S.; Chantratita, W.; Parasuk, W.; Sompornpisut, P.; Hannongbua, S. Insights into Saquinavir Resistance in the G48V HIV-1 Protease: Quantum Calculations and Molecular Dynamic Simulations Biophys. J. 2005, 88, 867-879 10.1529/biophysj.104.046110
-
(2005)
Biophys. J.
, vol.88
, pp. 867-879
-
-
Wittayanarakul, K.1
Aruksakunwong, O.2
Saen-Oon, S.3
Chantratita, W.4
Parasuk, W.5
Sompornpisut, P.6
Hannongbua, S.7
-
229
-
-
35448952558
-
Insight into Analysis of Interactions of Saquinavir with HIV-1 Protease in Comparison between the Wild-Type and G48V and G48V/L90M Mutants Based on QM and QM/MM Calculations
-
Saen-oon, S.; Aruksakunwong, O.; Wittayanarakul, K.; Sompornpisut, P.; Hannongbua, S. Insight Into Analysis of Interactions of Saquinavir with HIV-1 Protease in Comparison between the Wild-Type and G48V and G48V/L90M Mutants Based on QM and QM/MM Calculations J. Mol. Graphics Modell. 2007, 26, 720-727 10.1016/j.jmgm.2007.04.009
-
(2007)
J. Mol. Graphics Modell.
, vol.26
, pp. 720-727
-
-
Saen-Oon, S.1
Aruksakunwong, O.2
Wittayanarakul, K.3
Sompornpisut, P.4
Hannongbua, S.5
-
230
-
-
1542377504
-
Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: An Evaluation for Known Test Systems
-
Beierlein, F.; Lanig, H.; Schürer, G.; Horn, A. H. C.; Clark, T. Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: An Evaluation for Known Test Systems Mol. Phys. 2003, 101, 2469-2480 10.1080/0026897031000092940
-
(2003)
Mol. Phys.
, vol.101
, pp. 2469-2480
-
-
Beierlein, F.1
Lanig, H.2
Schürer, G.3
Horn, A.H.C.4
Clark, T.5
-
231
-
-
84912569558
-
Toward on-the-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function
-
Chaskar, P.; Zoete, V.; Röhrig, U. F. Toward on-the-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function J. Chem. Inf. Model. 2014, 54, 3137-3152 10.1021/ci5004152
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 3137-3152
-
-
Chaskar, P.1
Zoete, V.2
Röhrig, U.F.3
-
232
-
-
42449130535
-
Hepatitis C Virus NS5B Polymerase: QM/MM Calculations Show the Important Role of the Internal Energy in Ligand Binding
-
Parks, J. M.; Kondru, R. K.; Hu, H.; Beratan, D. N.; Yang, W. Hepatitis C Virus NS5B Polymerase: QM/MM Calculations Show the Important Role of the Internal Energy in Ligand Binding J. Phys. Chem. B 2008, 112, 3168-3176 10.1021/jp076885j
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3168-3176
-
-
Parks, J.M.1
Kondru, R.K.2
Hu, H.3
Beratan, D.N.4
Yang, W.5
-
233
-
-
79952582249
-
Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase
-
Burger, S. K.; Thompson, D. C.; Ayers, P. W. Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase J. Chem. Inf. Model. 2011, 51, 93-101 10.1021/ci100329z
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 93-101
-
-
Burger, S.K.1
Thompson, D.C.2
Ayers, P.W.3
-
234
-
-
67650149263
-
QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors
-
Gleeson, M. P.; Gleeson, D. QM/MM As a Tool in Fragment Based Drug Discovery. A Cross-Docking, Rescoring Study of Kinase Inhibitors J. Chem. Inf. Model. 2009, 49, 1437-1448 10.1021/ci900022h
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1437-1448
-
-
Gleeson, M.P.1
Gleeson, D.2
-
235
-
-
84969633749
-
-
Cambridge Crystallography Data Centre Software Ltd. Cambridge, England
-
GOLD; Cambridge Crystallography Data Centre Software Ltd.: Cambridge, England, 2013.
-
(2013)
GOLD
-
-
-
236
-
-
70350448289
-
Quantum Mechanical Scoring for Protein Docking
-
Cho, A. E.; Chung, J. Y.; Kim, M.; Park, K. Quantum Mechanical Scoring for Protein Docking J. Chem. Phys. 2009, 131, 134108 10.1063/1.3239504
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 134108
-
-
Cho, A.E.1
Chung, J.Y.2
Kim, M.3
Park, K.4
-
237
-
-
78751569971
-
Why OppA Protein can Bind Sequence-independent Peptides? A Combination of QM/MM, PB/SA, and Structure-based QSAR Analyses
-
Tian, F.; Yang, L.; Lv, F.; Luo, X.; Pan, Y. Why OppA Protein can Bind Sequence-independent Peptides? A Combination of QM/MM, PB/SA, and Structure-based QSAR Analyses Amino Acids 2011, 40, 493-503 10.1007/s00726-010-0661-9
-
(2011)
Amino Acids
, vol.40
, pp. 493-503
-
-
Tian, F.1
Yang, L.2
Lv, F.3
Luo, X.4
Pan, Y.5
-
238
-
-
84855201786
-
Characterization of PDZ Domain-peptide Interactions using an Integrated Protocol of QM/MM, PB/SA, and CFEA Analyses
-
Tian, F.; Lv, F.; Zhou, P.; Yang, L. Characterization of PDZ Domain-peptide Interactions using an Integrated Protocol of QM/MM, PB/SA, and CFEA Analyses J. Comput.-Aided Mol. Des. 2011, 25, 947-958 10.1007/s10822-011-9474-5
-
(2011)
J. Comput.-Aided Mol. Des.
, vol.25
, pp. 947-958
-
-
Tian, F.1
Lv, F.2
Zhou, P.3
Yang, L.4
-
239
-
-
84864953419
-
Strain Energy in Enzyme-Substrate Binding: An Energetic Insight into the Flexibility Versus Rigidity of Enzyme Active Site
-
Guo, X.; He, D.; Huang, L.; Liu, L.; Liu, L.; Yang, H. Strain Energy in Enzyme-Substrate Binding: An Energetic Insight Into the Flexibility Versus Rigidity of Enzyme Active Site Comput. Theor. Chem. 2012, 995, 17-23 10.1016/j.comptc.2012.06.017
-
(2012)
Comput. Theor. Chem.
, vol.995
, pp. 17-23
-
-
Guo, X.1
He, D.2
Huang, L.3
Liu, L.4
Liu, L.5
Yang, H.6
-
240
-
-
84861674509
-
Use of QM/MM Scheme to Reproduce Macromolecule-Small Molecule Noncovalent Binding Energy
-
Guo, X.; He, D.; Liu, L.; Kuang, R.; Liu, L. Use of QM/MM Scheme to Reproduce Macromolecule-Small Molecule Noncovalent Binding Energy Comput. Theor. Chem. 2012, 991, 134-140 10.1016/j.comptc.2012.04.010
-
(2012)
Comput. Theor. Chem.
, vol.991
, pp. 134-140
-
-
Guo, X.1
He, D.2
Liu, L.3
Kuang, R.4
Liu, L.5
-
241
-
-
33846191945
-
Rank-ordering Protein-Ligand binding Affinity by a Quantum Mechanics/Molecular Mechanics/Poisson-Boltzmann-Surface Area Model
-
Wang, M.; Wong, C. F. Rank-ordering Protein-Ligand binding Affinity by a Quantum Mechanics/Molecular Mechanics/Poisson-Boltzmann-Surface Area Model J. Chem. Phys. 2007, 126, 026101 10.1063/1.2423029
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 026101
-
-
Wang, M.1
Wong, C.F.2
-
242
-
-
84903601129
-
A Systematic Profile of Clinical Inhibitors Responsive to EGFR Somatic Amino Acid Mutations in Lung Cancer: Implication for the Molecular Mechanism of Drug Resistance and Sensitivity
-
Ai, X.; Sun, Y.; Wang, H.; Lu, S. A Systematic Profile of Clinical Inhibitors Responsive to EGFR Somatic Amino Acid Mutations in Lung Cancer: Implication for the Molecular Mechanism of Drug Resistance and Sensitivity Amino Acids 2014, 46, 1635-1648 10.1007/s00726-014-1716-0
-
(2014)
Amino Acids
, vol.46
, pp. 1635-1648
-
-
Ai, X.1
Sun, Y.2
Wang, H.3
Lu, S.4
-
243
-
-
84902911430
-
Testing the Sensitivities of Noncognate Inhibitors to Varicella Zoster Virus Thymidine Kinase: Implications for Postherpetic Neuralgia Therapy with Existing Agents
-
Yang, L.; Mo, X.; Yang, H.; Dai, H.; Tan, F. Testing the Sensitivities of Noncognate Inhibitors to Varicella Zoster Virus Thymidine Kinase: Implications for Postherpetic Neuralgia Therapy with Existing Agents J. Mol. Model. 2014, 20, 2321 10.1007/s00894-014-2321-6
-
(2014)
J. Mol. Model.
, vol.20
, pp. 2321
-
-
Yang, L.1
Mo, X.2
Yang, H.3
Dai, H.4
Tan, F.5
-
244
-
-
84906914562
-
Investigations on the Mechanisms of Interactions between Matrix Metalloproteinase 9 and Its Flavonoid Inhibitors Using A Combination of Molecular Docking, Hybrid Quantum Mechanical/Molecular Mechanical Calculations, and Molecular Dynamics Simulations
-
Zhou, Z.-G.; Yao, Q.-Z.; Lei, D.; Zhang, Q.-Q.; Zhang, J. Investigations on the Mechanisms of Interactions between Matrix Metalloproteinase 9 and Its Flavonoid Inhibitors Using A Combination of Molecular Docking, Hybrid Quantum Mechanical/Molecular Mechanical Calculations, and Molecular Dynamics Simulations Can. J. Chem. 2014, 92, 821-830 10.1139/cjc-2014-0180
-
(2014)
Can. J. Chem.
, vol.92
, pp. 821-830
-
-
Zhou, Z.-G.1
Yao, Q.-Z.2
Lei, D.3
Zhang, Q.-Q.4
Zhang, J.5
-
245
-
-
77957954013
-
Mixed Quantum Mechanics/Molecular Mechanics Scoring Frunction to Predict Protein-Ligand Binding affinity
-
Hayik, S. A.; Dunbrack, R.; Merz, K. M. Mixed Quantum Mechanics/Molecular Mechanics Scoring Frunction to Predict Protein-Ligand Binding affinity J. Chem. Theory Comput. 2010, 6, 3079-3091 10.1021/ct100315g
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3079-3091
-
-
Hayik, S.A.1
Dunbrack, R.2
Merz, K.M.3
-
246
-
-
0942276314
-
A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
-
Raha, K.; Merz, K. M. A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding J. Am. Chem. Soc. 2004, 126, 1020-1021 10.1021/ja038496i
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 1020-1021
-
-
Raha, K.1
Merz, K.M.2
-
247
-
-
84876848837
-
Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines
-
Brahmkshatriya, P. S.; Dobes, P.; Fanfrlik, J.; Rezac, J.; Paruch, K.; Bronowska, A.; Lepsík, M.; Hobza, P. Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines Curr. Comput.-Aided Drug Des. 2013, 9, 118-131 10.2174/1573409911309010011
-
(2013)
Curr. Comput.-Aided Drug Des.
, vol.9
, pp. 118-131
-
-
Brahmkshatriya, P.S.1
Dobes, P.2
Fanfrlik, J.3
Rezac, J.4
Paruch, K.5
Bronowska, A.6
Lepsík, M.7
Hobza, P.8
-
248
-
-
77957291978
-
A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands
-
Fanfrlík, J.; Bronowska, A. K.; Rezác, J.; Prenosil, O.; Konvalinka, J.; Hobza, P. A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands J. Phys. Chem. B 2010, 114, 12666-12678 10.1021/jp1032965
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 12666-12678
-
-
Fanfrlík, J.1
Bronowska, A.K.2
Rezác, J.3
Prenosil, O.4
Konvalinka, J.5
Hobza, P.6
-
249
-
-
84887901729
-
Modulation of Aldose Reductase Inhibition by Halogen Bond Tuning
-
Fanfrlík, J.; Kolár, M.; Kamlar, M.; Hurný, D.; Ruiz, F. X.; Cousido-Siah, A.; Mitschler, A.; Rezác, J.; Munusamy, E.; Lepsík, M.; Matejícek, P.; Veselý, J.; Podjarny, A.; Hobza, P. Modulation of Aldose Reductase Inhibition by Halogen Bond Tuning ACS Chem. Biol. 2013, 8, 2484-2492 10.1021/cb400526n
-
(2013)
ACS Chem. Biol.
, vol.8
, pp. 2484-2492
-
-
Fanfrlík, J.1
Kolár, M.2
Kamlar, M.3
Hurný, D.4
Ruiz, F.X.5
Cousido-Siah, A.6
Mitschler, A.7
Rezác, J.8
Munusamy, E.9
Lepsík, M.10
Matejícek, P.11
Veselý, J.12
Podjarny, A.13
Hobza, P.14
-
250
-
-
84937120472
-
The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition
-
Fanfrlík, J.; Ruiz, F. X.; Kadlcíková, A.; Rezác, J.; Cousido-Siah, A.; Mitschler, A.; Haldar, S.; Lepsík, M.; Kolár, M.; Majer, P.; Podjarny, A.; Hobza, P. A. The Effect of Halogen-to-Hydrogen Bond Substitution on Human Aldose Reductase Inhibition ACS Chem. Biol. 2015, 10, 1637-1642 10.1021/acschembio.5b00151
-
(2015)
ACS Chem. Biol.
, vol.10
, pp. 1637-1642
-
-
Fanfrlík, J.1
Ruiz, F.X.2
Kadlcíková, A.3
Rezác, J.4
Cousido-Siah, A.5
Mitschler, A.6
Haldar, S.7
Lepsík, M.8
Kolár, M.9
Majer, P.10
Podjarny, A.11
Hobza, P.A.12
-
251
-
-
0036774776
-
Ligand-Receptor Interaction at the Neural Nicotinic Acetylcholine Binding Site: A Theoretical Model
-
Morreale, A.; Maseras, F.; Iriepa, I.; Gálvez, E. Ligand-Receptor Interaction at the Neural Nicotinic Acetylcholine Binding Site: A Theoretical Model J. Mol. Graphics Modell. 2002, 21, 111-118 10.1016/S1093-3263(02)00127-4
-
(2002)
J. Mol. Graphics Modell.
, vol.21
, pp. 111-118
-
-
Morreale, A.1
Maseras, F.2
Iriepa, I.3
Gálvez, E.4
-
252
-
-
80051550298
-
Quantum Mechanics Study of the Hydroxyethylamines-BACE-1 Active Site Interaction Energies
-
Gueto-Tettay, C.; Drosos, J. C.; Vivas-Reyes, R. Quantum Mechanics Study of the Hydroxyethylamines-BACE-1 Active Site Interaction Energies J. Comput.-Aided Mol. Des. 2011, 25, 583-597 10.1007/s10822-011-9443-z
-
(2011)
J. Comput.-Aided Mol. Des.
, vol.25
, pp. 583-597
-
-
Gueto-Tettay, C.1
Drosos, J.C.2
Vivas-Reyes, R.3
-
253
-
-
84874646837
-
The MM2QM Tool for Combining Docking, Molecular Dynamics, Molecular Mechanics, and Quantum Mechanics
-
Nowosielski, M.; Hoffmann, M.; Kuron, A.; Korycka-Machala, M.; Dziadek, J. The MM2QM Tool for Combining Docking, Molecular Dynamics, Molecular Mechanics, and Quantum Mechanics J. Comput. Chem. 2013, 34, 750-756 10.1002/jcc.23192
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 750-756
-
-
Nowosielski, M.1
Hoffmann, M.2
Kuron, A.3
Korycka-Machala, M.4
Dziadek, J.5
-
254
-
-
79952141712
-
Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine
-
Nowosielski, M.; Hoffmann, M.; Wyrwicz, L. S.; Stepniak, P.; Plewczynski, D. M.; Lazniewski, M.; Ginalski, K.; Rychlewski, L. Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine J. Chem. Inf. Model. 2011, 51, 455-462 10.1021/ci100403b
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 455-462
-
-
Nowosielski, M.1
Hoffmann, M.2
Wyrwicz, L.S.3
Stepniak, P.4
Plewczynski, D.M.5
Lazniewski, M.6
Ginalski, K.7
Rychlewski, L.8
-
255
-
-
77954114200
-
High-Throughput Virtual Screening Using Quantum Mechanical Probes: Discovery of Selective Kinase Inhibitors. Chem
-
Zhou, T.; Caflisch, A. High-Throughput Virtual Screening Using Quantum Mechanical Probes: Discovery of Selective Kinase Inhibitors. Chem ChemMedChem 2010, 5, 1007-1014 10.1002/cmdc.201000085
-
(2010)
ChemMedChem
, vol.5
, pp. 1007-1014
-
-
Zhou, T.1
Caflisch, A.2
-
256
-
-
84879115826
-
Nonfitting Protein-Ligand Interaction Scoring Function Based on First-Principles Theoretical Chemistry Methods: Development and Application on Kinase Inhibitors
-
Rao, L.; Zhang, I. Y.; Guo, W.; Feng, L.; Meggers, E.; Xu, X. Nonfitting Protein-Ligand Interaction Scoring Function Based on First-Principles Theoretical Chemistry Methods: Development and Application on Kinase Inhibitors J. Comput. Chem. 2013, 34, 1636-1646 10.1002/jcc.23303
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 1636-1646
-
-
Rao, L.1
Zhang, I.Y.2
Guo, W.3
Feng, L.4
Meggers, E.5
Xu, X.6
-
257
-
-
77957018618
-
XO: An Extended ONIOM Method for Accurate and Efficient Geometry Optimization of Large Molecules
-
Guo, W. P.; Wu, A. A.; Xu, X. XO: An Extended ONIOM Method for Accurate and Efficient Geometry Optimization of Large Molecules Chem. Phys. Lett. 2010, 498, 203-208 10.1016/j.cplett.2010.08.033
-
(2010)
Chem. Phys. Lett.
, vol.498
, pp. 203-208
-
-
Guo, W.P.1
Wu, A.A.2
Xu, X.3
-
258
-
-
80052398418
-
Pairwise Additivity of Energy Components in Protein-Ligand Binding: The HIV II Protease Indinavir Case
-
Ucisik, M. N.; Dashti, D. S.; Faver, J. C.; Merz, K. M. Pairwise Additivity of Energy Components in Protein-Ligand Binding: The HIV II Protease Indinavir Case J. Chem. Phys. 2011, 135, 085101 10.1063/1.3624750
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 085101
-
-
Ucisik, M.N.1
Dashti, D.S.2
Faver, J.C.3
Merz, K.M.4
-
259
-
-
0344493816
-
New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy
-
Zhang, D. W.; Xiang, Y.; Zhang, J. Z. H. New Advance in Computational Chemistry: Full Quantum Mechanical ab Initio Computation of Streptavidin-Biotin Interaction Energy J. Phys. Chem. B 2003, 107, 12039-12041 10.1021/jp0359081
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 12039-12041
-
-
Zhang, D.W.1
Xiang, Y.2
Zhang, J.Z.H.3
-
260
-
-
1142279661
-
Quantum Mechanical Map for Protein-ligand Binding with Application to ß-trypsinO-benzamidine Complex
-
Zhang, D. W.; Xiang, Y.; Gao, A. M.; Zhang, J. Z. H. Quantum Mechanical Map for Protein-ligand Binding with Application to ß-trypsinO-benzamidine Complex J. Chem. Phys. 2004, 120, 1145-1148 10.1063/1.1639152
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 1145-1148
-
-
Zhang, D.W.1
Xiang, Y.2
Gao, A.M.3
Zhang, J.Z.H.4
-
261
-
-
4043162081
-
Fully Quantum Mechanical Energy Optimization for Protein-Ligand Structure
-
Xiang, Y.; Zhang, D. W.; Zhang, J. Z. H. Fully Quantum Mechanical Energy Optimization for Protein-Ligand Structure J. Comput. Chem. 2004, 25, 1431-1437 10.1002/jcc.20069
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1431-1437
-
-
Xiang, Y.1
Zhang, D.W.2
Zhang, J.Z.H.3
-
262
-
-
19944365281
-
Full Quantum Mechanical Study of Binding of HIV-1 Protease Drugs
-
Zhang, D. W.; Zhang, J. Z. H. Full Quantum Mechanical Study of Binding of HIV-1 Protease Drugs Int. J. Quantum Chem. 2005, 103, 246-257 10.1002/qua.20488
-
(2005)
Int. J. Quantum Chem.
, vol.103
, pp. 246-257
-
-
Zhang, D.W.1
Zhang, J.Z.H.2
-
263
-
-
17944362049
-
Quantum Study of Mutational Effect in Binding of Efavirenz to HIV-1 RT
-
Mei, Y.; He, X.; Xiang, Y.; Zhang, D. W.; Zhang, J. Z. H. Quantum Study of Mutational Effect in Binding of Efavirenz to HIV-1 RT Proteins: Struct., Funct., Genet. 2005, 59, 489-495 10.1002/prot.20455
-
(2005)
Proteins: Struct., Funct., Genet.
, vol.59
, pp. 489-495
-
-
Mei, Y.1
He, X.2
Xiang, Y.3
Zhang, D.W.4
Zhang, J.Z.H.5
-
264
-
-
36348986753
-
On the Accurate Reproduction of Ab Initio Interaction Energies between an Enzyme and Substrate
-
Bettens, R. P. A.; Lee, A. M. On the Accurate Reproduction of Ab Initio Interaction Energies between an Enzyme and Substrate Chem. Phys. Lett. 2007, 449, 341-346 10.1016/j.cplett.2007.10.073
-
(2007)
Chem. Phys. Lett.
, vol.449
, pp. 341-346
-
-
Bettens, R.P.A.1
Lee, A.M.2
-
265
-
-
52349091108
-
Quantum Mechanical Studies of Residue-Specific Hydrophobic Interactions in P53-MDM2 Binding
-
Ding, Y.; Mei, Y.; Zhang, J. Z. H. Quantum Mechanical Studies of Residue-Specific Hydrophobic Interactions in P53-MDM2 Binding J. Phys. Chem. B 2008, 112, 11396-11401 10.1021/jp8015886
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 11396-11401
-
-
Ding, Y.1
Mei, Y.2
Zhang, J.Z.H.3
-
266
-
-
84555179043
-
Explaining Statin Inhibition Effectiveness of HMG-Coa Reductase by Quantum Biochemistry Computations
-
da Costa, R. F.; Freire, V. N.; Bezerra, E. M.; Cavada, B. S.; Caetano, E. W. S.; De Lima Filho, J. L.; Albuquerque, E. L. Explaining Statin Inhibition Effectiveness of HMG-Coa Reductase by Quantum Biochemistry Computations Phys. Chem. Chem. Phys. 2012, 14, 1389-1398 10.1039/C1CP22824B
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 1389-1398
-
-
Da Costa, R.F.1
Freire, V.N.2
Bezerra, E.M.3
Cavada, B.S.4
Caetano, E.W.S.5
De Lima Filho, J.L.6
Albuquerque, E.L.7
-
267
-
-
84881582371
-
An ab initio Explanation of the Activation and Antagonism Strenth of an AMPA-Sensitive Glutamate Receptor
-
Martins, A. C. V.; De Lima-Neto, P.; Barroso-Neto, I. L.; Cavada, B. S.; Freire, V. N.; Caetano, E. W. S. An ab initio Explanation of the Activation and Antagonism Strenth of an AMPA-Sensitive Glutamate Receptor RSC Adv. 2013, 3, 14988-14992 10.1039/c3ra42149j
-
(2013)
RSC Adv.
, vol.3
, pp. 14988-14992
-
-
Martins, A.C.V.1
De Lima-Neto, P.2
Barroso-Neto, I.L.3
Cavada, B.S.4
Freire, V.N.5
Caetano, E.W.S.6
-
268
-
-
84873706554
-
Quantum Biochemistry Study of the T3-785 Tropocollagen Triple Helical Structure
-
Rodrigues, C. R. F.; Oliveira, J. I. N.; Fulco, U. L.; Albuquerque, E. L.; Moura, R. M.; Caetano, E. W. S.; Freire, V. N. Quantum Biochemistry Study of the T3-785 Tropocollagen Triple Helical Structure Chem. Phys. Lett. 2013, 559, 88-93 10.1016/j.cplett.2012.12.061
-
(2013)
Chem. Phys. Lett.
, vol.559
, pp. 88-93
-
-
Rodrigues, C.R.F.1
Oliveira, J.I.N.2
Fulco, U.L.3
Albuquerque, E.L.4
Moura, R.M.5
Caetano, E.W.S.6
Freire, V.N.7
-
269
-
-
84902658137
-
The Quantum Biophysics of the Isoniazid Adduct NADH Binding to Its Inha Reductase Target
-
da Silva Ribeiro, T. C.; da Costa, R. F.; Bezerra, E. M.; Freire, V. N.; Lyra, M. L.; Manzoni, V. The Quantum Biophysics of the Isoniazid Adduct NADH Binding to Its Inha Reductase Target New J. Chem. 2014, 38, 2946-2957 10.1039/c3nj01453c
-
(2014)
New J. Chem.
, vol.38
, pp. 2946-2957
-
-
Da Silva Ribeiro, T.C.1
Da Costa, R.F.2
Bezerra, E.M.3
Freire, V.N.4
Lyra, M.L.5
Manzoni, V.6
-
270
-
-
84907985812
-
Antipsychotic Haloperidol Binding to the Human Dopamine D3 Receptor: Beyond Docking Through QM/MM Refinement Toward the Design of Improved Schizophrenia Medicines
-
Zanatta, G.; Nunes, G.; Bezerra, E. M.; da Costa, R. F.; Martins, A.; Caetano, E. W. S.; Freire, V. N.; Gottfried, C. Antipsychotic Haloperidol Binding to the Human Dopamine D3 Receptor: Beyond Docking Through QM/MM Refinement Toward the Design of Improved Schizophrenia Medicines ACS Chem. Neurosci. 2014, 5, 1041-1054 10.1021/cn500111e
-
(2014)
ACS Chem. Neurosci.
, vol.5
, pp. 1041-1054
-
-
Zanatta, G.1
Nunes, G.2
Bezerra, E.M.3
Da Costa, R.F.4
Martins, A.5
Caetano, E.W.S.6
Freire, V.N.7
Gottfried, C.8
-
271
-
-
84930942335
-
Quantum Molecular Modelling of Ibuprofen Bound to Human Serum Albumin
-
Dantas, D. S.; Oliveira, J. I. N.; Lima Neto, J. X.; da Costa, R. F.; Bezerra, E. M.; Freire, V. N.; Caetano, E. W. S.; Fulco, U. L.; Albuquerque, E. L. Quantum Molecular Modelling of Ibuprofen Bound to Human Serum Albumin RSC Adv. 2015, 5, 49439-49450 10.1039/C5RA04395F
-
(2015)
RSC Adv.
, vol.5
, pp. 49439-49450
-
-
Dantas, D.S.1
Oliveira, J.I.N.2
Lima Neto, J.X.3
Da Costa, R.F.4
Bezerra, E.M.5
Freire, V.N.6
Caetano, E.W.S.7
Fulco, U.L.8
Albuquerque, E.L.9
-
272
-
-
84862566881
-
Fully Ab Initio Protein-Ligand Interaction Energies with Dispersion Corrected Density-Functional Theory
-
Antony, J.; Grimme, S. Fully Ab Initio Protein-Ligand Interaction Energies with Dispersion Corrected Density-Functional Theory J. Comput. Chem. 2012, 33, 1730-1739 10.1002/jcc.23004
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1730-1739
-
-
Antony, J.1
Grimme, S.2
-
273
-
-
68649091295
-
Calculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects
-
Söderhjelm, P.; Aquilante, F.; Ryde, U. Calculation of Protein-Ligand Interaction Energies by a Fragmentation Approach Combining High-Level Quantum Chemistry with Classical Many-Body Effects J. Phys. Chem. B 2009, 113, 11085-11094 10.1021/jp810551h
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 11085-11094
-
-
Söderhjelm, P.1
Aquilante, F.2
Ryde, U.3
-
274
-
-
84941114007
-
Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems
-
Andrejic, M.; Ryde, U.; Mata, R.; Söderhjelm, P. Coupled-Cluster Interaction Energies for 200-Atom Host-Guest Systems ChemPhysChem 2014, 15, 3270-3281 10.1002/cphc.201402379
-
(2014)
ChemPhysChem
, vol.15
, pp. 3270-3281
-
-
Andrejic, M.1
Ryde, U.2
Mata, R.3
Söderhjelm, P.4
-
275
-
-
11144282711
-
Ab Initio Quantum Mechanical Study of the Binding Energies of Human Estrogen Receptor with Its Ligands: An Application of Fragment Molecular Orbital Method
-
Fukuzawa, K.; Kitaura, K.; Uebayasi, M.; Nakata, K.; Kaminuma, T.; Nakano, T. Ab Initio Quantum Mechanical Study of the Binding Energies of Human Estrogen Receptor with Its Ligands: An Application of Fragment Molecular Orbital Method J. Comput. Chem. 2005, 26, 1-10 10.1002/jcc.20130
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1-10
-
-
Fukuzawa, K.1
Kitaura, K.2
Uebayasi, M.3
Nakata, K.4
Kaminuma, T.5
Nakano, T.6
-
276
-
-
33244464010
-
VISCANA: Visualized Cluster Analysis of Protein- Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening
-
Amari, S.; Aizawa, M.; Zhang, J.; Fukuzawa, K.; Mochizuki, Y.; Iwasawa, Y.; Nakata, K.; Chuman, H.; Nakano, T. VISCANA: Visualized Cluster Analysis of Protein- Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening J. Chem. Inf. Model. 2006, 46, 221-230 10.1021/ci050262q
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 221-230
-
-
Amari, S.1
Aizawa, M.2
Zhang, J.3
Fukuzawa, K.4
Mochizuki, Y.5
Iwasawa, Y.6
Nakata, K.7
Chuman, H.8
Nakano, T.9
-
277
-
-
33748626264
-
Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method
-
Fukuzawa, K.; Mochizuki, Y.; Tanaka, S.; Kitaura, K.; Nakano, T. Molecular Interactions between Estrogen Receptor and Its Ligand Studied by the ab Initio Fragment Molecular Orbital Method J. Phys. Chem. B 2006, 110, 16102-16110 10.1021/jp060770i
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 16102-16110
-
-
Fukuzawa, K.1
Mochizuki, Y.2
Tanaka, S.3
Kitaura, K.4
Nakano, T.5
-
278
-
-
77954762254
-
Interactions between 1 Alpha,25(OH)(2)D-3 and Residues in the Ligand-Binding Pocket of the Vitamin D Receptor: A Correlated Fragment Molecular Orbital Study
-
Yamagishi, K.; Tokiwa, H.; Makishima, M.; Yamada, S. Interactions between 1 Alpha,25(OH)(2)D-3 and Residues in the Ligand-Binding Pocket of the Vitamin D Receptor: A Correlated Fragment Molecular Orbital Study J. Steroid Biochem. Mol. Biol. 2010, 121, 63-67 10.1016/j.jsbmb.2010.03.028
-
(2010)
J. Steroid Biochem. Mol. Biol.
, vol.121
, pp. 63-67
-
-
Yamagishi, K.1
Tokiwa, H.2
Makishima, M.3
Yamada, S.4
-
279
-
-
77953292378
-
Flexible Ligand Recognition of Peroxisome Proliferator-Activated Receptor-Gamma (PPAR Gamma)
-
Yamagishi, K.; Yamamoto, K.; Mochizuki, Y.; Nakano, T.; Yamada, S.; Tokiwa, H. Flexible Ligand Recognition of Peroxisome Proliferator-Activated Receptor-Gamma (PPAR Gamma) Bioorg. Med. Chem. Lett. 2010, 20, 3344-3347 10.1016/j.bmcl.2010.04.031
-
(2010)
Bioorg. Med. Chem. Lett.
, vol.20
, pp. 3344-3347
-
-
Yamagishi, K.1
Yamamoto, K.2
Mochizuki, Y.3
Nakano, T.4
Yamada, S.5
Tokiwa, H.6
-
280
-
-
34247486968
-
Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator: Roles of Helix 12 in the Coactivator Binding Mechanism
-
Ito, M.; Fukuzawa, K.; Mochizuki, Y.; Nakano, T.; Tanaka, S. Ab Initio Fragment Molecular Orbital Study of Molecular Interactions between Liganded Retinoid X Receptor and Its Coactivator: Roles of Helix 12 in the Coactivator Binding Mechanism J. Phys. Chem. B 2007, 111, 3525-3533 10.1021/jp070054w
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 3525-3533
-
-
Ito, M.1
Fukuzawa, K.2
Mochizuki, Y.3
Nakano, T.4
Tanaka, S.5
-
281
-
-
33646586407
-
Intra-and Intermolecular Interactions between Cyclic-AMP Receptor Protein and DNA: Ab Initio Fragment Molecular Orbital Study
-
Fukuzawa, K.; Komeiji, Y.; Mochizuki, Y.; Kato, A.; Nakano, T.; Tanaka, S. Intra-and Intermolecular Interactions between Cyclic-AMP Receptor Protein and DNA: Ab Initio Fragment Molecular Orbital Study J. Comput. Chem. 2006, 27, 948-960 10.1002/jcc.20399
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 948-960
-
-
Fukuzawa, K.1
Komeiji, Y.2
Mochizuki, Y.3
Kato, A.4
Nakano, T.5
Tanaka, S.6
-
282
-
-
81555211242
-
Prediction of Probable Mutations in Influenza Virus Hemagglutinin Protein Based on Large-Scale Ab Initio Fragment Molecular Orbital Calculations
-
Yoshioka, A.; Fukuzawa, K.; Mochizuki, Y.; Yamashita, K.; Nakano, T.; Okiyama, Y.; Nobusawa, E.; Nakajima, K.; Tanaka, S. Prediction of Probable Mutations in Influenza Virus Hemagglutinin Protein Based on Large-Scale Ab Initio Fragment Molecular Orbital Calculations J. Mol. Graphics Modell. 2011, 30, 110-119 10.1016/j.jmgm.2011.06.011
-
(2011)
J. Mol. Graphics Modell.
, vol.30
, pp. 110-119
-
-
Yoshioka, A.1
Fukuzawa, K.2
Mochizuki, Y.3
Yamashita, K.4
Nakano, T.5
Okiyama, Y.6
Nobusawa, E.7
Nakajima, K.8
Tanaka, S.9
-
283
-
-
84879967419
-
Interaction Analysis of HIV-1 Antibody 2G12 and Man9GlcNAc2 Ligand: Theoretical Calculations by Fragment Molecular Orbital and MD Methods
-
Koyama, T.; Ueno-Noto, K.; Takano, K. Interaction Analysis of HIV-1 Antibody 2G12 and Man9GlcNAc2 Ligand: Theoretical Calculations by Fragment Molecular Orbital and MD Methods Chem. Phys. Lett. 2013, 578, 144-149 10.1016/j.cplett.2013.06.009
-
(2013)
Chem. Phys. Lett.
, vol.578
, pp. 144-149
-
-
Koyama, T.1
Ueno-Noto, K.2
Takano, K.3
-
284
-
-
33847239926
-
Influenza Viral Hemagglutinin Complicated Shape Is Advantageous to Its Binding Affinity for Sialosaccharide Receptor
-
Sawada, T.; Hashimoto, T.; Nakano, H.; Suzuki, T.; Suzuki, Y.; Kawaoka, Y.; Ishida, H.; Kiso, M. Influenza Viral Hemagglutinin Complicated Shape Is Advantageous to Its Binding Affinity for Sialosaccharide Receptor Biochem. Biophys. Res. Commun. 2007, 355, 6-9 10.1016/j.bbrc.2006.12.239
-
(2007)
Biochem. Biophys. Res. Commun.
, vol.355
, pp. 6-9
-
-
Sawada, T.1
Hashimoto, T.2
Nakano, H.3
Suzuki, T.4
Suzuki, Y.5
Kawaoka, Y.6
Ishida, H.7
Kiso, M.8
-
285
-
-
34249884543
-
Molecular Recognition Mechanism of FK506 Binding Protein: An All-Electron Fragment Molecular Orbital Study
-
Nakanishi, I.; Fedorov, D. G.; Kitaura, K. Molecular Recognition Mechanism of FK506 Binding Protein: An All-Electron Fragment Molecular Orbital Study Proteins: Struct., Funct., Genet. 2007, 68, 145-158 10.1002/prot.21389
-
(2007)
Proteins: Struct., Funct., Genet.
, vol.68
, pp. 145-158
-
-
Nakanishi, I.1
Fedorov, D.G.2
Kitaura, K.3
-
286
-
-
78649521266
-
Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect
-
Sawada, T.; Fedorov, D. G.; Kitaura, K. Binding of Influenza A Virus Hemagglutinin to the Sialoside Receptor Is Not Controlled by the Homotropic Allosteric Effect J. Phys. Chem. B 2010, 114, 15700-15705 10.1021/jp1068895
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 15700-15705
-
-
Sawada, T.1
Fedorov, D.G.2
Kitaura, K.3
-
287
-
-
79751471221
-
Prediction of Cyclin-Dependent Kinase 2 Inhibitor Potency Using the Fragment Molecular Orbital Method
-
Mazanetz, M. P.; Ichihara, O.; Law, R. J.; Whittaker, M. Prediction of Cyclin-Dependent Kinase 2 Inhibitor Potency Using the Fragment Molecular Orbital Method J. Cheminf. 2011, 3, 2 10.1186/1758-2946-3-2
-
(2011)
J. Cheminf.
, vol.3
, pp. 2
-
-
Mazanetz, M.P.1
Ichihara, O.2
Law, R.J.3
Whittaker, M.4
-
288
-
-
84923863074
-
Thermodynamics of Binding of Di- and Tetrasubstituted Naphthalene Diimide Ligands to DNA G-Quadruplex
-
Prato, G.; Silvent, S.; Saka, S.; Lamberto, M.; Kosenkov, D. Thermodynamics of Binding of Di- and Tetrasubstituted Naphthalene Diimide Ligands to DNA G-Quadruplex J. Phys. Chem. B 2015, 119, 3335-3347 10.1021/jp509637y
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 3335-3347
-
-
Prato, G.1
Silvent, S.2
Saka, S.3
Lamberto, M.4
Kosenkov, D.5
-
289
-
-
80052021439
-
Specific Interactions and Binding Free Energies between Thermolysin and Dipeptides: Molecular Simulations Combined with Ab Initio Molecular Orbital and Classical Vibrational Analysis
-
Dedachi, K.; Hirakawa, T.; Fujita, S.; Khan, M. T. H.; Sylte, I.; Kurita, N. Specific Interactions and Binding Free Energies between Thermolysin and Dipeptides: Molecular Simulations Combined with Ab Initio Molecular Orbital and Classical Vibrational Analysis J. Comput. Chem. 2011, 32, 3047-3057 10.1002/jcc.21887
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 3047-3057
-
-
Dedachi, K.1
Hirakawa, T.2
Fujita, S.3
Khan, M.T.H.4
Sylte, I.5
Kurita, N.6
-
290
-
-
84855217449
-
Specific Interactions and Binding Energies between Thermolysin and Potent Inhibitors: Molecular Simulations Based on Ab Initio Molecular Orbital Method
-
Hirakawa, T.; Fujita, S.; Ohyama, T.; Dedachi, K.; Khan, M. T. H.; Sylte, I.; Kurita, N. Specific Interactions and Binding Energies between Thermolysin and Potent Inhibitors: Molecular Simulations Based on Ab Initio Molecular Orbital Method J. Mol. Graphics Modell. 2012, 33, 1-11 10.1016/j.jmgm.2011.10.006
-
(2012)
J. Mol. Graphics Modell.
, vol.33
, pp. 1-11
-
-
Hirakawa, T.1
Fujita, S.2
Ohyama, T.3
Dedachi, K.4
Khan, M.T.H.5
Sylte, I.6
Kurita, N.7
-
291
-
-
84908264622
-
Ab Initio Molecular Simulations for Proposing Potent Inhibitors to Butyrylcholinesterases
-
Murakawa, T.; Matsushita, Y.; Suzuki, T.; Khan, M. T. H.; Kurita, N. Ab Initio Molecular Simulations for Proposing Potent Inhibitors to Butyrylcholinesterases J. Mol. Graphics Modell. 2014, 54, 54-61 10.1016/j.jmgm.2014.09.002
-
(2014)
J. Mol. Graphics Modell.
, vol.54
, pp. 54-61
-
-
Murakawa, T.1
Matsushita, Y.2
Suzuki, T.3
Khan, M.T.H.4
Kurita, N.5
-
292
-
-
79957884348
-
The Effects of Amino-Acid Mutations on Specific Interactions between Urokinase-Type Plasminogen Activator and Its Receptor: Ab Initio Molecular Orbital Calculations
-
Tsuji, S.; Kasumi, T.; Nagase, K.; Yoshikawa, E.; Kobayashi, H.; Kurita, N. The Effects of Amino-Acid Mutations on Specific Interactions between Urokinase-Type Plasminogen Activator and Its Receptor: Ab Initio Molecular Orbital Calculations J. Mol. Graphics Modell. 2011, 29, 975-984 10.1016/j.jmgm.2011.04.003
-
(2011)
J. Mol. Graphics Modell.
, vol.29
, pp. 975-984
-
-
Tsuji, S.1
Kasumi, T.2
Nagase, K.3
Yoshikawa, E.4
Kobayashi, H.5
Kurita, N.6
-
293
-
-
84894664868
-
Affinity of HIV-1 Antibody 2G12 with Monosaccharides: A Theoretical Study Based on Explicit and Implicit Water Models
-
Koyama, Y.; Ueno-Noto, K.; Takano, K. Affinity of HIV-1 Antibody 2G12 with Monosaccharides: A Theoretical Study Based on Explicit and Implicit Water Models Comput. Biol. Chem. 2014, 49, 36-44 10.1016/j.compbiolchem.2014.01.013
-
(2014)
Comput. Biol. Chem.
, vol.49
, pp. 36-44
-
-
Koyama, Y.1
Ueno-Noto, K.2
Takano, K.3
-
294
-
-
84866332768
-
Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to A Solvated Griffithsin-Carbohydrate Complex
-
Nagata, T.; Fedorov, D. G.; Sawada, T.; Kitaura, K. Analysis of Solute-Solvent Interactions in the Fragment Molecular Orbital Method Interfaced with Effective Fragment Potentials: Theory and Application to A Solvated Griffithsin-Carbohydrate Complex J. Phys. Chem. A 2012, 116, 9088-9099 10.1021/jp304991a
-
(2012)
J. Phys. Chem. A
, vol.116
, pp. 9088-9099
-
-
Nagata, T.1
Fedorov, D.G.2
Sawada, T.3
Kitaura, K.4
-
295
-
-
84877343557
-
Proposal for an Inhibitor of Alzheimer's Disease Blocking Aggregation of Amyloid-B Peptides: Ab Initio Molecular Simulations
-
Okamoto, A.; Nomura, K.; Yano, A.; Higai, S.; Kondo, T.; Kamba, S.; Kurita, N. Proposal for an Inhibitor of Alzheimer's Disease Blocking Aggregation of Amyloid-B Peptides: Ab Initio Molecular Simulations J. Phys.: Conf. Ser. 2013, 433, 012033 10.1088/1742-6596/433/1/012033
-
(2013)
J. Phys.: Conf. Ser.
, vol.433
, pp. 012033
-
-
Okamoto, A.1
Nomura, K.2
Yano, A.3
Higai, S.4
Kondo, T.5
Kamba, S.6
Kurita, N.7
-
296
-
-
84866624195
-
An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method
-
Asada, N.; Fedorov, D. G.; Kitaura, K.; Nakanishi, I.; Merz, K. M. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method J. Phys. Chem. Lett. 2012, 3, 2604-2610 10.1021/jz3010688
-
(2012)
J. Phys. Chem. Lett.
, vol.3
, pp. 2604-2610
-
-
Asada, N.1
Fedorov, D.G.2
Kitaura, K.3
Nakanishi, I.4
Merz, K.M.5
-
297
-
-
4944222323
-
Application of Semiempirical Quantum Chemical Methods As A Scoring Function in Docking
-
Vasilyev, V.; Bliznyuk, A. Application of Semiempirical Quantum Chemical Methods As A Scoring Function in Docking Theor. Chem. Acc. 2004, 112, 313-317 10.1007/s00214-004-0589-9
-
(2004)
Theor. Chem. Acc.
, vol.112
, pp. 313-317
-
-
Vasilyev, V.1
Bliznyuk, A.2
-
298
-
-
1942540506
-
A Quantum Mechanical Study on Phosphotyrosyl Peptide Binding to the SH2 Domain of P56lck Tyrosine Kinase with Insights into the Biochemistry of Intracellular Signal Transduction Events
-
Pichierri, F. A Quantum Mechanical Study on Phosphotyrosyl Peptide Binding to the SH2 Domain of P56lck Tyrosine Kinase with Insights Into the Biochemistry of Intracellular Signal Transduction Events Biophys. Chem. 2004, 109, 295-304 10.1016/j.bpc.2003.12.006
-
(2004)
Biophys. Chem.
, vol.109
, pp. 295-304
-
-
Pichierri, F.1
-
299
-
-
18144377355
-
Quantum Chemical Study on the Affinity Maturation of 48G7 Antibody
-
Ohno, K.; Wada, M.; Saito, S.; Inoue, Y.; Sakurai, M. Quantum Chemical Study on the Affinity Maturation of 48G7 Antibody J. Mol. Struct.: THEOCHEM 2005, 722, 203-211 10.1016/j.theochem.2004.11.061
-
(2005)
J. Mol. Struct.: THEOCHEM
, vol.722
, pp. 203-211
-
-
Ohno, K.1
Wada, M.2
Saito, S.3
Inoue, Y.4
Sakurai, M.5
-
300
-
-
70350635655
-
A Quantum Mechanical Approach to Ligand Binding - Calculation of Ligand-Protein Binding Affinities for Stromelysin-1 (MMP-3) Inhibitors
-
Li, J.; Reynolds, C. H. A Quantum Mechanical Approach to Ligand Binding - Calculation of Ligand-Protein Binding Affinities for Stromelysin-1 (MMP-3) Inhibitors Can. J. Chem. 2009, 87, 1480-1484 10.1139/V09-129
-
(2009)
Can. J. Chem.
, vol.87
, pp. 1480-1484
-
-
Li, J.1
Reynolds, C.H.2
-
301
-
-
84873717393
-
Assessment of the Free Binding Energy of 1,25-Dihydroxyvitamin D3 and Its Analogs with the Human VDR Receptor Model
-
Kamel, K.; Kolinski, A. Assessment of the Free Binding Energy of 1,25-Dihydroxyvitamin D3 and Its Analogs with the Human VDR Receptor Model Acta Biochim. Pol. 2012, 59, 653-660
-
(2012)
Acta Biochim. Pol.
, vol.59
, pp. 653-660
-
-
Kamel, K.1
Kolinski, A.2
-
302
-
-
47749108669
-
Is Quantum Mechanics Necessary for Predicting Binding Free Energy?
-
Zhou, T.; Huang, D.; Caflisch, A. Is Quantum Mechanics Necessary for Predicting Binding Free Energy? J. Med. Chem. 2008, 51, 4280-4288 10.1021/jm800242q
-
(2008)
J. Med. Chem.
, vol.51
, pp. 4280-4288
-
-
Zhou, T.1
Huang, D.2
Caflisch, A.3
-
303
-
-
68749106989
-
A Fast Method of Large-Scale Serial Semiempirical Calculations of Docking Complexes
-
Anikin, N. A.; Andreev, A. M.; Kuz'minskii, M. B.; Mendkovich, A. S. A Fast Method of Large-Scale Serial Semiempirical Calculations of Docking Complexes Russ. Chem. Bull. 2008, 57, 1793-1798 10.1007/s11172-008-0241-2
-
(2008)
Russ. Chem. Bull.
, vol.57
, pp. 1793-1798
-
-
Anikin, N.A.1
Andreev, A.M.2
Kuz'Minskii, M.B.3
Mendkovich, A.S.4
-
304
-
-
64549162370
-
QM/QM Docking Method Based on the Variational Finite Localized Molecular Orbital Approximation
-
Anisimov, V. M.; Bugaenko, V. L. QM/QM Docking Method Based on the Variational Finite Localized Molecular Orbital Approximation J. Comput. Chem. 2009, 30, 784-798 10.1002/jcc.21100
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 784-798
-
-
Anisimov, V.M.1
Bugaenko, V.L.2
-
305
-
-
60749128002
-
Combining A Genetic Algorithm with A Linear Scaling Semiempirical Method for Protein-Ligand Docking
-
Thiriot, E.; Monard, G. Combining A Genetic Algorithm with A Linear Scaling Semiempirical Method for Protein-Ligand Docking J. Mol. Struct.: THEOCHEM 2009, 898, 31-41 10.1016/j.theochem.2008.12.041
-
(2009)
J. Mol. Struct.: THEOCHEM
, vol.898
, pp. 31-41
-
-
Thiriot, E.1
Monard, G.2
-
306
-
-
84890851685
-
AlgoGen: A Tool Coupling A Linear-Scaling Quantum Method with A Genetic Algorithm for Exploring Non-Covalent Interactions
-
Barberot, C.; Boisson, J. C.; Gérard, S.; Khartabil, H.; Thiriot, E.; Monard, G.; Hénon, E. AlgoGen: A Tool Coupling A Linear-Scaling Quantum Method with A Genetic Algorithm for Exploring Non-Covalent Interactions Comput. Theor. Chem. 2014, 1028, 7-18 10.1016/j.comptc.2013.11.020
-
(2014)
Comput. Theor. Chem.
, vol.1028
, pp. 7-18
-
-
Barberot, C.1
Boisson, J.C.2
Gérard, S.3
Khartabil, H.4
Thiriot, E.5
Monard, G.6
Hénon, E.7
-
307
-
-
18644382069
-
Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction
-
Raha, K.; Van der Vaart, A. J.; Riley, K. E.; Peters, M. B.; Westerhoff, L. M.; Kim, H.; Merz, K. M. Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein-Ligand Interaction J. Am. Chem. Soc. 2005, 127, 6583-6594 10.1021/ja042666p
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 6583-6594
-
-
Raha, K.1
Van Der Vaart, A.J.2
Riley, K.E.3
Peters, M.B.4
Westerhoff, L.M.5
Kim, H.6
Merz, K.M.7
-
308
-
-
22244451417
-
Large-Scale Validation of A Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of A Diverse Set of Protein-Ligand Complexes
-
Raha, K.; Merz, K. M. Large-Scale Validation of A Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of A Diverse Set of Protein-Ligand Complexes J. Med. Chem. 2005, 48, 4558-4575 10.1021/jm048973n
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4558-4575
-
-
Raha, K.1
Merz, K.M.2
-
309
-
-
77951997313
-
Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design
-
Zhang, X.; Gibbs, A. C.; Reynolds, C. H.; Peters, M. B.; Westerhoff, L. M. Quantum Mechanical Pairwise Decomposition Analysis of Protein Kinase B Inhibitors: Validating a New Tool for Guiding Drug Design J. Chem. Inf. Model. 2010, 50, 651-661 10.1021/ci9003333
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 651-661
-
-
Zhang, X.1
Gibbs, A.C.2
Reynolds, C.H.3
Peters, M.B.4
Westerhoff, L.M.5
-
310
-
-
84863088606
-
Prediction of Trypsin/Molecular Fragment Binding Affinities by Free Energy Decomposition and Empirical Scores
-
Benson, M. L.; Faver, J. C.; Ucisik, M. N.; Dashti, D. S.; Zheng, Z.; Merz, K. M. Prediction of Trypsin/Molecular Fragment Binding Affinities by Free Energy Decomposition and Empirical Scores J. Comput.-Aided Mol. Des. 2012, 26, 647-659 10.1007/s10822-012-9567-9
-
(2012)
J. Comput.-Aided Mol. Des.
, vol.26
, pp. 647-659
-
-
Benson, M.L.1
Faver, J.C.2
Ucisik, M.N.3
Dashti, D.S.4
Zheng, Z.5
Merz, K.M.6
-
311
-
-
79955395664
-
Transferable Scoring Function Based on Semiempirical Quantum Mechanical PM6-DH2Method: CDK2 with 15 Structurally Diverse Inhibitors
-
Dobes, P.; Fanfrlík, J.; Rezác, J.; Otyepka, M.; Hobza, P. Transferable Scoring Function Based on Semiempirical Quantum Mechanical PM6-DH2Method: CDK2 with 15 Structurally Diverse Inhibitors J. Comput.-Aided Mol. Des. 2011, 25, 223-235 10.1007/s10822-011-9413-5
-
(2011)
J. Comput.-Aided Mol. Des.
, vol.25
, pp. 223-235
-
-
Dobes, P.1
Fanfrlík, J.2
Rezác, J.3
Otyepka, M.4
Hobza, P.5
-
312
-
-
79959921557
-
Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, while the Empirical Potential Fails
-
Dobes, P.; Rezác, J.; Fanfrlík, J.; Otyepka, M.; Hobza, P. Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails J. Phys. Chem. B 2011, 115, 8581-8589 10.1021/jp202149z
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 8581-8589
-
-
Dobes, P.1
Rezác, J.2
Fanfrlík, J.3
Otyepka, M.4
Hobza, P.5
-
313
-
-
84890040875
-
Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma Mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors
-
Fanfrlík, J.; Brahmkshatriya, P. S.; Rezác, J.; Jílková, A. M.; Horn, M.; Mares, M.; Hobza, P.; Lepsík, M. Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma Mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors J. Phys. Chem. B 2013, 117, 14973-14982 10.1021/jp409604n
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 14973-14982
-
-
Fanfrlík, J.1
Brahmkshatriya, P.S.2
Rezác, J.3
Jílková, A.M.4
Horn, M.5
Mares, M.6
Hobza, P.7
Lepsík, M.8
-
314
-
-
0002760331
-
On the Role of Covalent Strain in Protein Function
-
Research Signpost: Trivandrum, India
-
Ryde, U. On the Role of Covalent Strain in Protein Function. Recent Research Developments in Protein Engineering; Research Signpost: Trivandrum, India, 2002; Vol. 2, pp 65-91.
-
(2002)
Recent Research Developments in Protein Engineering
, vol.2
, pp. 65-91
-
-
Ryde, U.1
-
315
-
-
0032112610
-
Conformational Energy Penalties of Protein-bound Ligands
-
Boström, J.; Norrby, P.-O.; Liljefors, T. Conformational Energy Penalties of Protein-bound Ligands J. Comput.-Aided Mol. Des. 1998, 12, 383-396 10.1023/A:1008007507641
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 383-396
-
-
Boström, J.1
Norrby, P.-O.2
Liljefors, T.3
-
316
-
-
84859191545
-
PDB Ligand Conformational Energies Calculated Quantum-mechanically
-
Sitzmann, M.; Weidlich, I. E.; Filippov, I. V.; Liao, C.; Peach, M. L.; Ihlenfeldt, W.-D.; Karki, R. G.; Borodina, Y. V.; Cachau, R. E.; Nicklaus, M. C. PDB Ligand Conformational Energies Calculated Quantum-mechanically J. Chem. Inf. Model. 2012, 52, 739-756 10.1021/ci200595n
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 739-756
-
-
Sitzmann, M.1
Weidlich, I.E.2
Filippov, I.V.3
Liao, C.4
Peach, M.L.5
Ihlenfeldt, W.-D.6
Karki, R.G.7
Borodina, Y.V.8
Cachau, R.E.9
Nicklaus, M.C.10
-
317
-
-
79959695225
-
Accurate Assessment of the Strain Energy in a Protein-bound Drug using QM/MM X-ray Refinement and Converged Quantum Chemistry
-
Fu, Z.; Li, X.; Merz, K. M. Accurate Assessment of the Strain Energy in a Protein-bound Drug using QM/MM X-ray Refinement and Converged Quantum Chemistry J. Comput. Chem. 2011, 32, 2587-2597 10.1002/jcc.21838
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 2587-2597
-
-
Fu, Z.1
Li, X.2
Merz, K.M.3
-
318
-
-
84885627179
-
Structural Relaxation and Binding Energy Calculations of FK506 Binding Protein Complexes using the Large-scale DFT Code CONQUEST
-
Otsuka, T.; Okimoto, N.; Taiji, M.; Bowler, D. R.; Miyazaki, T. Structural Relaxation and Binding Energy Calculations of FK506 Binding Protein Complexes using the Large-scale DFT Code CONQUEST J. Phys.: Conf. Ser. 2013, 454, 012057 10.1088/1742-6596/454/1/012057
-
(2013)
J. Phys.: Conf. Ser.
, vol.454
, pp. 012057
-
-
Otsuka, T.1
Okimoto, N.2
Taiji, M.3
Bowler, D.R.4
Miyazaki, T.5
-
319
-
-
20344362412
-
Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics
-
Gräter, F.; Schwarzl, S. M.; Dejaegere, A.; Fischer, S.; Smith, J. C. Protein/Ligand Binding Free Energies Calculated with Quantum Mechanics/Molecular Mechanics J. Phys. Chem. B 2005, 109, 10474-10483 10.1021/jp044185y
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 10474-10483
-
-
Gräter, F.1
Schwarzl, S.M.2
Dejaegere, A.3
Fischer, S.4
Smith, J.C.5
-
320
-
-
66149094168
-
Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach
-
Retegan, M.; Milet, A.; Jamet, H. Exploring the Binding of Inhibitors Derived from Tetrabromobenzimidazole to the CK2 Protein Using a QM/MM-PB/SA Approach J. Chem. Inf. Model. 2009, 49, 963-971 10.1021/ci8004435
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 963-971
-
-
Retegan, M.1
Milet, A.2
Jamet, H.3
-
321
-
-
80054898012
-
Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study
-
Ibrahim, M. A. A. Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study J. Chem. Inf. Model. 2011, 51, 2549-2559 10.1021/ci2002582
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2549-2559
-
-
Ibrahim, M.A.A.1
-
322
-
-
78751612997
-
Binding Free Energy Calculation with QM/MM Hybrid methods for Abl-Kinase inhibitor
-
Dubey, K. D.; Ojha, R. P. Binding Free Energy Calculation with QM/MM Hybrid methods for Abl-Kinase inhibitor J. Biol. Phys. 2011, 37, 69-78 10.1007/s10867-010-9199-z
-
(2011)
J. Biol. Phys.
, vol.37
, pp. 69-78
-
-
Dubey, K.D.1
Ojha, R.P.2
-
323
-
-
84896507252
-
Insights from QM/MM Modeling the 3D Structure of the 2009 H1N1 Influenza A Virus Neuraminidase and Its Binding Interactions with Antiviral Drugs
-
Wang, Y.-T.; Chen, Y.-C. Insights from QM/MM Modeling the 3D Structure of the 2009 H1N1 Influenza A Virus Neuraminidase and Its Binding Interactions with Antiviral Drugs Mol. Inf. 2014, 33, 240-249 10.1002/minf.201300117
-
(2014)
Mol. Inf.
, vol.33
, pp. 240-249
-
-
Wang, Y.-T.1
Chen, Y.-C.2
-
324
-
-
84856725232
-
Is Inhibition Process Better Described with MD(QM/MM) Simulations? the Case of Urokinase Type Plasminogen Activator Inhibitors
-
Barbault, F.; Maurel, F. Is Inhibition Process Better Described with MD(QM/MM) Simulations? The Case of Urokinase Type Plasminogen Activator Inhibitors J. Comput. Chem. 2012, 33, 607-616 10.1002/jcc.21983
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 607-616
-
-
Barbault, F.1
Maurel, F.2
-
325
-
-
84904760980
-
-
University of California: San Francisco
-
Case, D. A.; Babin, V.; Berryman, J. T.; Betz, R. M.; Cai, Q.; Cerutti, D. S.; Cheatham, T. E.; Darden, T. A.; Duke, R. E.; Gohlke, H.; et al., AMBER 14; University of California: San Francisco, 2014.
-
(2014)
AMBER 14
-
-
Case, D.A.1
Babin, V.2
Berryman, J.T.3
Betz, R.M.4
Cai, Q.5
Cerutti, D.S.6
Cheatham, T.E.7
Darden, T.A.8
Duke, R.E.9
Gohlke, H.10
-
326
-
-
42149100111
-
The Implementation of A Fast and Accurate QM/MM Potential Method in Amber
-
Walker, R. C.; Crowley, M. F.; Case, D. A. The Implementation of A Fast and Accurate QM/MM Potential Method in Amber J. Comput. Chem. 2008, 29, 1019-1031 10.1002/jcc.20857
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 1019-1031
-
-
Walker, R.C.1
Crowley, M.F.2
Case, D.A.3
-
327
-
-
84896961990
-
Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors
-
Wichapong, K.; Rohe, A.; Platzer, C.; Slynko, I.; Erdmann, F.; Schmidt, M.; Sippl, W. Application of Docking and QM/MM-GBSA Rescoring to Screen for Novel Myt1 Kinase Inhibitors J. Chem. Inf. Model. 2014, 54, 881-893 10.1021/ci4007326
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 881-893
-
-
Wichapong, K.1
Rohe, A.2
Platzer, C.3
Slynko, I.4
Erdmann, F.5
Schmidt, M.6
Sippl, W.7
-
328
-
-
54249114557
-
A QM/MM-PBSA Method to Estimate Free Energies for Reactions in Proteins
-
Kaukonen, M.; Söderhjelm, P.; Heimdal, J.; Ryde, U. A QM/MM-PBSA Method to Estimate Free Energies for Reactions in Proteins J. Phys. Chem. B 2008, 112, 12537-12548 10.1021/jp802648k
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 12537-12548
-
-
Kaukonen, M.1
Söderhjelm, P.2
Heimdal, J.3
Ryde, U.4
-
329
-
-
84969731907
-
QM/MM calculations on proteins
-
in press
-
Ryde, U. QM/MM calculations on proteins. Methods Enzymol., 2016, in press.
-
(2016)
Methods Enzymol.
-
-
Ryde, U.1
-
330
-
-
77952723365
-
Characterization of the Structures of Phosphodiesterase 10 Binding with Adenosine 3′,5′-Monophosphate and Guanosine 3′,5′-Monophosphate by Hybrid Quantum Mechanical/ Molecular Mechanical Calculations
-
Lu, H.; Goren, A. C.; Zhan, C.-G. Characterization of the Structures of Phosphodiesterase 10 Binding with Adenosine 3′,5′-Monophosphate and Guanosine 3′,5′-Monophosphate by Hybrid Quantum Mechanical/ Molecular Mechanical Calculations J. Phys. Chem. B 2010, 114, 7022-7028 10.1021/jp911527y
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 7022-7028
-
-
Lu, H.1
Goren, A.C.2
Zhan, C.-G.3
-
331
-
-
80054908133
-
Fundamental Reaction Pathway and Free Energy Profile for Hydrolysis of Intracellular Second Messenger Adenosine 30,50-Cyclic Monophosphate (cAMP) Catalyzed by Phosphodiesterase
-
Chen, X.; Zhao, X.; Xiong, Y.; Liu, J.; Zhan, C.-G. Fundamental Reaction Pathway and Free Energy Profile for Hydrolysis of Intracellular Second Messenger Adenosine 30,50-Cyclic Monophosphate (cAMP) Catalyzed by Phosphodiesterase J. Phys. Chem. B 2011, 115, 12208-12219 10.1021/jp205509w
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 12208-12219
-
-
Chen, X.1
Zhao, X.2
Xiong, Y.3
Liu, J.4
Zhan, C.-G.5
-
332
-
-
84897388634
-
Binding Free Energies for Nicotine Analogs Inhibiting Cytochrome P450 2A6 by A Combined Use of Molecular Dynamics Simulations and QM/MM-PBSA Calculations
-
Lu, H.; Huang, X.; AbdulHameed, M. D. M.; Zhan, C.-G. Binding Free Energies for Nicotine Analogs Inhibiting Cytochrome P450 2A6 by A Combined Use of Molecular Dynamics Simulations and QM/MM-PBSA Calculations Bioorg. Med. Chem. 2014, 22, 2149-2156 10.1016/j.bmc.2014.02.037
-
(2014)
Bioorg. Med. Chem.
, vol.22
, pp. 2149-2156
-
-
Lu, H.1
Huang, X.2
AbdulHameed, M.D.M.3
Zhan, C.-G.4
-
333
-
-
84859420868
-
2OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why
-
2OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why Chem. Biol. Drug Des. 2012, 79, 663-673 10.1111/j.1747-0285.2012.01349.x
-
(2012)
Chem. Biol. Drug Des.
, vol.79
, pp. 663-673
-
-
Manta, S.1
Xipnitou, A.2
Kiritsis, C.3
Kantsadi, A.L.4
Hayes, J.M.5
Skamnaki, V.T.6
Lamprakis, C.7
Kontou, M.8
Zoumpoulakis, P.9
Zographos, S.E.10
-
334
-
-
84859181463
-
The Sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides Towards Glycogen Phosphorylase B
-
Kantsadi, A. L.; Hayes, J. M.; Manta, S.; Skamnaki, V. T.; Kiritsis, C.; Psarra, A. M.; Koutsogiannis, Z.; Dimopoulou, A.; Theofanous, S.; Nikoleousakos, N. et al. The Sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides Towards Glycogen Phosphorylase B ChemMedChem 2012, 7, 722-732 10.1002/cmdc.201100533
-
(2012)
ChemMedChem
, vol.7
, pp. 722-732
-
-
Kantsadi, A.L.1
Hayes, J.M.2
Manta, S.3
Skamnaki, V.T.4
Kiritsis, C.5
Psarra, A.M.6
Koutsogiannis, Z.7
Dimopoulou, A.8
Theofanous, S.9
Nikoleousakos, N.10
-
335
-
-
84888830305
-
Sourcing the Affinity of Flavonoids for the Glycogen Phosphorylase Inhibitor Site Via Crystallography, Kinetics and QM/MM-PBSA Binding Studies: Comparison of Chrysin and Flavopiridol
-
Tsitsanou, K. E.; Hayes, J. M.; Keramioti, M.; Mamais, M.; Oikonomakos, N. G.; Kato, A.; Leonidas, D. D.; Zographos, S. E. Sourcing the Affinity of Flavonoids for the Glycogen Phosphorylase Inhibitor Site Via Crystallography, Kinetics and QM/MM-PBSA Binding Studies: Comparison of Chrysin and Flavopiridol Food Chem. Toxicol. 2013, 61, 14-27 10.1016/j.fct.2012.12.030
-
(2013)
Food Chem. Toxicol.
, vol.61
, pp. 14-27
-
-
Tsitsanou, K.E.1
Hayes, J.M.2
Keramioti, M.3
Mamais, M.4
Oikonomakos, N.G.5
Kato, A.6
Leonidas, D.D.7
Zographos, S.E.8
-
336
-
-
77952337364
-
Ligand Affinities Estimated by Quantum Chemical Calculations
-
Söderhjelm, P.; Kongsted, J.; Ryde, U. Ligand Affinities Estimated by Quantum Chemical Calculations J. Chem. Theory Comput. 2010, 6, 1726-1737 10.1021/ct9006986
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1726-1737
-
-
Söderhjelm, P.1
Kongsted, J.2
Ryde, U.3
-
337
-
-
78149448036
-
Nonpolar Solvation Free Energies of Protein-Ligand Complexes
-
Genheden, S.; Kongsted, J.; Söderhjelm, P.; Ryde, U. Nonpolar Solvation Free Energies of Protein-Ligand Complexes J. Chem. Theory Comput. 2010, 6, 3558-3568 10.1021/ct100272s
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3558-3568
-
-
Genheden, S.1
Kongsted, J.2
Söderhjelm, P.3
Ryde, U.4
-
338
-
-
80051775090
-
Accurate Predictions of Non-Polar Solvation Free Energies Require Explicit Consideration of Binding Site Hydration
-
Genheden, S.; Mikulskis, P.; Hu, L.; Kongsted, J.; Söderhjelm, P.; Ryde, U. Accurate Predictions of Non-Polar Solvation Free Energies Require Explicit Consideration of Binding Site Hydration J. Am. Chem. Soc. 2011, 133, 13081-13092 10.1021/ja202972m
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 13081-13092
-
-
Genheden, S.1
Mikulskis, P.2
Hu, L.3
Kongsted, J.4
Söderhjelm, P.5
Ryde, U.6
-
339
-
-
84874057542
-
A Theoretical Study of the Two Binding Modes between Lysozyme and Tri-NAG with an Explicit Solvent Model Based on the Fragment Molecular Orbital Method
-
Ishikawa, T.; Burri, R. R.; Kamatari, Y. O.; Sakuraba, S.; Matubayasi, N.; Kitao, A.; Kuwata, K. A Theoretical Study of the Two Binding Modes between Lysozyme and Tri-NAG with an Explicit Solvent Model Based on the Fragment Molecular Orbital Method Phys. Chem. Chem. Phys. 2013, 15, 3646-3654 10.1039/c3cp42761g
-
(2013)
Phys. Chem. Chem. Phys.
, vol.15
, pp. 3646-3654
-
-
Ishikawa, T.1
Burri, R.R.2
Kamatari, Y.O.3
Sakuraba, S.4
Matubayasi, N.5
Kitao, A.6
Kuwata, K.7
-
340
-
-
84872980312
-
Quantum Chemical Study on Molecular-Level Affinity of DJ-1 Binding Compounds
-
Shigemitsu, Y. Quantum Chemical Study on Molecular-Level Affinity of DJ-1 Binding Compounds Int. J. Quantum Chem. 2013, 113, 574-579 10.1002/qua.24132
-
(2013)
Int. J. Quantum Chem.
, vol.113
, pp. 574-579
-
-
Shigemitsu, Y.1
-
341
-
-
13444302257
-
Molecular dynamics simulaions of the TEM-1 ß-lactamase complexed with cephalothin
-
Díaz, N.; Suárez, D.; Merz, K. M.; Sordo, T. L. Molecular dynamics simulaions of the TEM-1 ß-lactamase complexed with cephalothin J. Med. Chem. 2005, 48, 780-791 10.1021/jm0493663
-
(2005)
J. Med. Chem.
, vol.48
, pp. 780-791
-
-
Díaz, N.1
Suárez, D.2
Merz, K.M.3
Sordo, T.L.4
-
342
-
-
79958183335
-
Quantum Mechanical Binding Free Energy Calculation for Phosphopeptide Inhibitors of the Lck SH2 domiain
-
Anisimov, V. M.; Cavasotto, C. N. Quantum Mechanical Binding Free Energy Calculation for Phosphopeptide Inhibitors of the Lck SH2 domiain J. Comput. Chem. 2011, 32, 2254-2263 10.1002/jcc.21808
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 2254-2263
-
-
Anisimov, V.M.1
Cavasotto, C.N.2
-
343
-
-
84855187820
-
Computational and Experimental Studies of the Interaction between Phospho-peptides and the C-terminal Domain of BRCA
-
Anisimov, V. M.; Ziemys, A.; Kizhake, S.; Yuan, Z.; Natarajan, A.; Cavasotto, C. N. Computational and Experimental Studies of the Interaction between Phospho-peptides and the C-terminal Domain of BRCA J. Comput.-Aided Mol. Des. 2011, 25, 1071-1084 10.1007/s10822-011-9484-3
-
(2011)
J. Comput.-Aided Mol. Des.
, vol.25
, pp. 1071-1084
-
-
Anisimov, V.M.1
Ziemys, A.2
Kizhake, S.3
Yuan, Z.4
Natarajan, A.5
Cavasotto, C.N.6
-
344
-
-
84860835748
-
A Semiempirical Approach to Ligand-Binding Affinities: Dependence on the Hamiltonian and Corrections
-
Mikulskis, P.; Genheden, S.; Wichmann, K.; Ryde, U. A Semiempirical Approach to Ligand-Binding Affinities: Dependence on the Hamiltonian and Corrections J. Comput. Chem. 2012, 33, 1179-1189 10.1002/jcc.22949
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1179-1189
-
-
Mikulskis, P.1
Genheden, S.2
Wichmann, K.3
Ryde, U.4
-
345
-
-
78751641417
-
Protein-Protein Interactions from Linear-Scaling First-Principles Quantum-Mechanical Calculations
-
Cole, D. J.; Skylaris, C.-K.; Rajendra, E.; Venkitaraman, A. R.; Payne, M. C. Protein-Protein Interactions From Linear-Scaling First-Principles Quantum-Mechanical Calculations EPL 2010, 91, 37004 10.1209/0295-5075/91/37004
-
(2010)
EPL
, vol.91
, pp. 37004
-
-
Cole, D.J.1
Skylaris, C.-K.2
Rajendra, E.3
Venkitaraman, A.R.4
Payne, M.C.5
-
346
-
-
79954561773
-
First Principles-Based Calculations of Free Energy of Binding: Application to Ligand Binding in a Self-Assembling Superstructure
-
Fox, S.; Wallnoefer, H. G.; Fox, T.; Tautermann, C. S.; Skylaris, C.-K. First Principles-Based Calculations of Free Energy of Binding: Application to Ligand Binding in a Self-Assembling Superstructure J. Chem. Theory Comput. 2011, 7, 1102-1108 10.1021/ct100706u
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1102-1108
-
-
Fox, S.1
Wallnoefer, H.G.2
Fox, T.3
Tautermann, C.S.4
Skylaris, C.-K.5
-
347
-
-
84928337487
-
Density Functional Theory Calculations on Entire Proteins for Free Energies of Binding: Application to A Model Polar Binding Site
-
Fox, S. J.; Dziedzic, J.; Fox, T.; Tautermann, C. S.; Skylaris, C.-K. Density Functional Theory Calculations on Entire Proteins for Free Energies of Binding: Application to A Model Polar Binding Site Proteins: Struct., Funct., Genet. 2014, 82, 3335-3346 10.1002/prot.24686
-
(2014)
Proteins: Struct., Funct., Genet.
, vol.82
, pp. 3335-3346
-
-
Fox, S.J.1
Dziedzic, J.2
Fox, T.3
Tautermann, C.S.4
Skylaris, C.-K.5
-
348
-
-
77953976984
-
An MM/3D-RISM Approach for Ligand-Binding Affinities
-
Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. An MM/3D-RISM Approach for Ligand-Binding Affinities J. Phys. Chem. B 2010, 114, 8505-8516 10.1021/jp101461s
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8505-8516
-
-
Genheden, S.1
Luchko, T.2
Gusarov, S.3
Kovalenko, A.4
Ryde, U.5
-
349
-
-
23944459025
-
A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands
-
Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D. M.; Raha, S.; Balaz, S. A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands J. Med. Chem. 2005, 48, 5437-5447 10.1021/jm049050v
-
(2005)
J. Med. Chem.
, vol.48
, pp. 5437-5447
-
-
Khandelwal, A.1
Lukacova, V.2
Comez, D.3
Kroll, D.M.4
Raha, S.5
Balaz, S.6
-
350
-
-
33947262611
-
Improved Estimation of Ligand-Macromolecule Binding Affinities by Linear Response Approach Using A Combination of Multi-Mode MD Simulation and QM/MM Methods
-
Khandelwal, A.; Balaz, S. Improved Estimation of Ligand-Macromolecule Binding Affinities by Linear Response Approach Using A Combination of Multi-Mode MD Simulation and QM/MM Methods J. Comput.-Aided Mol. Des. 2007, 21, 131-137 10.1007/s10822-007-9104-4
-
(2007)
J. Comput.-Aided Mol. Des.
, vol.21
, pp. 131-137
-
-
Khandelwal, A.1
Balaz, S.2
-
351
-
-
34548808607
-
QM/MM Linear Response Method Distinguishes Ligand Affinities for Closely Related Metalloproteins
-
Khandelwal, A.; Balaz, S. QM/MM Linear Response Method Distinguishes Ligand Affinities for Closely Related Metalloproteins Proteins: Struct., Funct., Genet. 2007, 69, 326-339 10.1002/prot.21500
-
(2007)
Proteins: Struct., Funct., Genet.
, vol.69
, pp. 326-339
-
-
Khandelwal, A.1
Balaz, S.2
-
352
-
-
84858011865
-
Binding Affinity Prediction for Ligands and Receptors Forming Tautomers and Ionization Species: Inhibition of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK2)
-
Natesan, S.; Subramaniam, R.; Bergeron, C.; Balaz, S. Binding Affinity Prediction for Ligands and Receptors Forming Tautomers and Ionization Species: Inhibition of Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MK2) J. Med. Chem. 2012, 55, 2035-2047 10.1021/jm201217q
-
(2012)
J. Med. Chem.
, vol.55
, pp. 2035-2047
-
-
Natesan, S.1
Subramaniam, R.2
Bergeron, C.3
Balaz, S.4
-
353
-
-
34748912966
-
A Quantum Mechanics/Molecular Mechanics Study of the Protein-Ligand Interaction for Inhibitors of HIV-1 Integrase
-
Alves, C. N.; Martí, S.; Castillo, R.; Andrés, J.; Moliner, V.; Tuñón, I.; Silla, E. A Quantum Mechanics/Molecular Mechanics Study of the Protein-Ligand Interaction for Inhibitors of HIV-1 Integrase Chem.-Eur. J. 2007, 13, 7715-7724 10.1002/chem.200700040
-
(2007)
Chem. - Eur. J.
, vol.13
, pp. 7715-7724
-
-
Alves, C.N.1
Martí, S.2
Castillo, R.3
Andrés, J.4
Moliner, V.5
Tuñón, I.6
Silla, E.7
-
354
-
-
34247359998
-
A Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues
-
Alves, C. N.; Martí, S.; Castillo, R.; Andrés, J.; Moliner, V.; Tuñón, I.; Silla, E. A Calculation of binding energy using BLYP/MM for the HIV-1 integrase complexed with the S-1360 and two analogues Bioorg. Med. Chem. 2007, 15, 3818-3824 10.1016/j.bmc.2007.03.027
-
(2007)
Bioorg. Med. Chem.
, vol.15
, pp. 3818-3824
-
-
Alves, C.N.1
Martí, S.2
Castillo, R.3
Andrés, J.4
Moliner, V.5
Tuñón, I.6
Silla, E.7
-
355
-
-
41649100340
-
A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid
-
Alves, C. N.; Martí, S.; Castillo, R.; Andrés, J.; Moliner, V.; Tuñón, I.; Silla, E. A Quantum Mechanic/Molecular Mechanic Study of the Wild-Type and N155S Mutant HIV-1 Integrase Complexed with Diketo Acid Biophys. J. 2008, 94, 2443-2451 10.1529/biophysj.107.107623
-
(2008)
Biophys. J.
, vol.94
, pp. 2443-2451
-
-
Alves, C.N.1
Martí, S.2
Castillo, R.3
Andrés, J.4
Moliner, V.5
Tuñón, I.6
Silla, E.7
-
356
-
-
33846426835
-
A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Predictor of the Biological Activity
-
Alzate-Morales, J. H.; Contreras, R.; Soriano, A.; Tuñon, I.; Silla, E. A Computational Study of the Protein-Ligand Interactions in CDK2 Inhibitors: Using Quantum Mechanics/Molecular Mechanics Interaction Energy as a Predictor of the Biological Activity Biophys. J. 2007, 92, 430-439 10.1529/biophysj.106.091512
-
(2007)
Biophys. J.
, vol.92
, pp. 430-439
-
-
Alzate-Morales, J.H.1
Contreras, R.2
Soriano, A.3
Tuñon, I.4
Silla, E.5
-
357
-
-
84870505941
-
Correlation between Biological Activity and Binding Energy in Systems of Integrin with Cyclic RGD-Containing Binders: A QM/MM Molecular Dynamics Study
-
Xiang, M.; Lin, Y.; He, G.; Chen, L.; Yang, M.; Yang, S.; Mo, Y. Correlation between Biological Activity and Binding Energy in Systems of Integrin with Cyclic RGD-Containing Binders: A QM/MM Molecular Dynamics Study J. Mol. Model. 2012, 18, 4917-4927 10.1007/s00894-012-1487-z
-
(2012)
J. Mol. Model.
, vol.18
, pp. 4917-4927
-
-
Xiang, M.1
Lin, Y.2
He, G.3
Chen, L.4
Yang, M.5
Yang, S.6
Mo, Y.7
-
358
-
-
54949153723
-
QSAR Study of Cyclic Urea Type HIV-1PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1PR
-
Yoshida, T.; Yamagishi, K.; Chuman, H. QSAR Study of Cyclic Urea Type HIV-1PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1PR QSAR Comb. Sci. 2008, 27, 694-703 10.1002/qsar.200730108
-
(2008)
QSAR Comb. Sci.
, vol.27
, pp. 694-703
-
-
Yoshida, T.1
Yamagishi, K.2
Chuman, H.3
-
359
-
-
77952772108
-
Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using Ab Initio MO Calculations on Their Complex Structures
-
Yoshida, T.; Munei, Y.; Hitaoka, S.; Chuman, H. Correlation Analyses on Binding Affinity of Substituted Benzenesulfonamides with Carbonic Anhydrase Using Ab Initio MO Calculations on Their Complex Structures J. Chem. Inf. Model. 2010, 50, 850-860 10.1021/ci100068w
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 850-860
-
-
Yoshida, T.1
Munei, Y.2
Hitaoka, S.3
Chuman, H.4
-
360
-
-
80054930148
-
Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures - LERE-QSAR Analysis (IV)
-
Hitaoka, S.; Matoba, H.; Harada, M.; Yoshida, T.; Tsuji, D.; Hirokawa, T.; Itoh, K.; Chuman, H. Correlation Analyses on Binding Affinity of Sialic Acid Analogues and Anti-Influenza Drugs with Human Neuraminidase Using ab Initio MO Calculations on Their Complex Structures-LERE-QSAR Analysis (IV) J. Chem. Inf. Model. 2011, 51, 2706-2716 10.1021/ci2002395
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2706-2716
-
-
Hitaoka, S.1
Matoba, H.2
Harada, M.3
Yoshida, T.4
Tsuji, D.5
Hirokawa, T.6
Itoh, K.7
Chuman, H.8
-
361
-
-
84902816202
-
Blind Prediction of SAMPL4 Cucurbit-7-Uril Binding Affinities with the Mining Minima Method
-
Muddana, H. S.; Yin, J.; Sapra, N. V.; Fenley, A. T.; Gilson, M. K. Blind Prediction of SAMPL4 Cucurbit-7-Uril Binding Affinities with the Mining Minima Method J. Comput.-Aided Mol. Des. 2014, 28, 463-474 10.1007/s10822-014-9726-2
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 463-474
-
-
Muddana, H.S.1
Yin, J.2
Sapra, N.V.3
Fenley, A.T.4
Gilson, M.K.5
-
362
-
-
34547688945
-
Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method
-
Reddy, M. R.; Erion, M. D. Relative Binding Affinities of Fructose-1,6-Bisphosphatase Inhibitors Calculated Using a Quantum Mechanics-Based Free Energy Perturbation Method J. Am. Chem. Soc. 2007, 129, 9296-9297 10.1021/ja072905j
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 9296-9297
-
-
Reddy, M.R.1
Erion, M.D.2
-
363
-
-
84856583630
-
Use of Quantum Mechanics/molecular Mechanics-based FEP Method for Calculating Relative Binding Affinities of FBPase Inhibitors for Type-2 Diabetes
-
Rathore, R. S.; Reddy, R. N.; Kondapi, A. K.; Reddanna, P.; Reddy, M. R. Use of Quantum Mechanics/molecular Mechanics-based FEP Method for Calculating Relative Binding Affinities of FBPase Inhibitors for Type-2 Diabetes Theor. Chem. Acc. 2012, 131, 1096 10.1007/s00214-012-1096-z
-
(2012)
Theor. Chem. Acc.
, vol.131
, pp. 1096
-
-
Rathore, R.S.1
Reddy, R.N.2
Kondapi, A.K.3
Reddanna, P.4
Reddy, M.R.5
-
364
-
-
84865454171
-
Theoretical studies of HIV-1 Reverse Transcriptase Inhibition
-
Swiderek, K.; Marti, S.; Moliner, V. Theoretical studies of HIV-1 Reverse Transcriptase Inhibition Phys. Chem. Chem. Phys. 2012, 14, 12614-12624 10.1039/c2cp40953d
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 12614-12624
-
-
Swiderek, K.1
Marti, S.2
Moliner, V.3
-
365
-
-
84986466995
-
Microscopic Models for Quantum Mechanical Calculations of Chemical Processes in Solutions: LD/AMPAC and SCAAS/AMPAC Calculations of Solvation Energies
-
Luzhkov, V.; Warshel, A. Microscopic Models for Quantum Mechanical Calculations of Chemical Processes in Solutions: LD/AMPAC and SCAAS/AMPAC Calculations of Solvation Energies J. Comput. Chem. 1992, 13, 199-213 10.1002/jcc.540130212
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 199-213
-
-
Luzhkov, V.1
Warshel, A.2
-
366
-
-
84923124949
-
Recent Advances in QM/MM Free Energy Calculations Using Reference Potentials
-
Duarte, F.; Amrein, B. A.; Blaha-Nelson, D.; Kamerlin, S. C. L. Recent Advances in QM/MM Free Energy Calculations Using Reference Potentials Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 954-965 10.1016/j.bbagen.2014.07.008
-
(2015)
Biochim. Biophys. Acta, Gen. Subj.
, vol.1850
, pp. 954-965
-
-
Duarte, F.1
Amrein, B.A.2
Blaha-Nelson, D.3
Kamerlin, S.C.L.4
-
367
-
-
79952501515
-
Non-Boltzmann Sampling and Bennett's Acceptance Ratio Method: How to Profit from Bending the Rules
-
König, G.; Boresch, S. Non-Boltzmann Sampling and Bennett's Acceptance Ratio Method: How to Profit from Bending the Rules J. Comput. Chem. 2011, 32, 1082-1090 10.1002/jcc.21687
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1082-1090
-
-
König, G.1
Boresch, S.2
-
368
-
-
43949083733
-
Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods
-
Hu, H.; Yang, W. Free Energies of Chemical Reactions in Solution and in Enzymes with Ab Initio Quantum Mechanics/Molecular Mechanics Methods Annu. Rev. Phys. Chem. 2008, 59, 573-601 10.1146/annurev.physchem.59.032607.093618
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.2
-
369
-
-
84865471425
-
Convergence of QM/MM Free-Energy Perturbations Based on Molecular-Mechanics or Semiempirical Simulations
-
Heimdal, J.; Ryde, U. Convergence of QM/MM Free-Energy Perturbations Based on Molecular-Mechanics or Semiempirical Simulations Phys. Chem. Chem. Phys. 2012, 14, 12592-12604 10.1039/c2cp41005b
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 12592-12604
-
-
Heimdal, J.1
Ryde, U.2
-
370
-
-
38049039241
-
An Efficient Method for the Calculation of Quantum Mechanics/Molecular Mechanics Free Energies
-
Woods, C. J.; Manby, F. R.; Mulholland, A. J. An Efficient Method for the Calculation of Quantum Mechanics/Molecular Mechanics Free Energies J. Chem. Phys. 2008, 128, 014109 10.1063/1.2805379
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 014109
-
-
Woods, C.J.1
Manby, F.R.2
Mulholland, A.J.3
-
371
-
-
84882305295
-
Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies
-
Fox, S. J.; Pittock, C.; Tautermann, C. S.; Fox, T.; Christ, C.; Malcolm, N. O. J.; Essex, J. W.; Skylaris, C.-K. Free Energies of Binding from Large-Scale First-Principles Quantum Mechanical Calculations: Application to Ligand Hydration Energies J. Phys. Chem. B 2013, 117, 9478-9485 10.1021/jp404518r
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 9478-9485
-
-
Fox, S.J.1
Pittock, C.2
Tautermann, C.S.3
Fox, T.4
Christ, C.5
Malcolm, N.O.J.6
Essex, J.W.7
Skylaris, C.-K.8
-
372
-
-
84899912778
-
Extensive all-atom Monte Carlo Sampling and QM/MM Corrections in the SAMPL4 Hydration Free energy Challenge
-
Genheden, S.; Cabedo Martinez, A. I.; Criddle, M. P.; Essex, J. W. Extensive all-atom Monte Carlo Sampling and QM/MM Corrections in the SAMPL4 Hydration Free energy Challenge J. Comput.-Aided Mol. Des. 2014, 28, 187-200 10.1007/s10822-014-9717-3
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 187-200
-
-
Genheden, S.1
Cabedo Martinez, A.I.2
Criddle, M.P.3
Essex, J.W.4
-
373
-
-
84899916134
-
Predicting Hydration Free Energies with A Hybrid QM/MM Approach: An Evaluation of Implicit and Explicit Solvation Models in SAMPL4
-
König, G.; Pickard, F. C.; Mei, Y.; Brooks, B. R. Predicting Hydration Free Energies with A Hybrid QM/MM Approach: An Evaluation of Implicit and Explicit Solvation Models in SAMPL4 J. Comput.-Aided Mol. Des. 2014, 28, 245-257 10.1007/s10822-014-9708-4
-
(2014)
J. Comput.-Aided Mol. Des.
, vol.28
, pp. 245-257
-
-
König, G.1
Pickard, F.C.2
Mei, Y.3
Brooks, B.R.4
-
374
-
-
84898491607
-
Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes
-
König, G.; Hudson, P. S.; Boresch, S.; Woodcock, H. L. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes J. Chem. Theory Comput. 2014, 10, 1406-1419 10.1021/ct401118k
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1406-1419
-
-
König, G.1
Hudson, P.S.2
Boresch, S.3
Woodcock, H.L.4
-
375
-
-
84935914842
-
A "stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration
-
Sampson, C.; Fox, T.; Tautermann, C. S.; Woods, C.; Skylaris, C.-K. A "Stepping Stone" Approach for Obtaining Quantum Free Energies of Hydration J. Phys. Chem. B 2015, 119, 7030-7040 10.1021/acs.jpcb.5b01625
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 7030-7040
-
-
Sampson, C.1
Fox, T.2
Tautermann, C.S.3
Woods, C.4
Skylaris, C.-K.5
-
376
-
-
79955509805
-
A Simple QM/MM Approach for Capturing Polarization Effects in Protein Ligand Binding Free Energy Calculations
-
Beierlein, F. R.; Michel, J.; Essex, J. W. A Simple QM/MM Approach for Capturing Polarization Effects in Protein Ligand Binding Free Energy Calculations J. Phys. Chem. B 2011, 115, 4911-4926 10.1021/jp109054j
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 4911-4926
-
-
Beierlein, F.R.1
Michel, J.2
Essex, J.W.3
-
377
-
-
84921527016
-
Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein-Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase
-
Woods, C. J.; Shaw, K. E.; Mulholland, A. J. Combined Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations for Protein-Ligand Complexes: Free Energies of Binding of Water Molecules in Influenza Neuraminidase J. Phys. Chem. B 2015, 119, 997-1001 10.1021/jp506413j
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 997-1001
-
-
Woods, C.J.1
Shaw, K.E.2
Mulholland, A.J.3
-
378
-
-
84939537729
-
Binding Affinities by Free-Energy Perturbation Using QM/MM with A Large QM System and Polarizable MM Model
-
Genheden, S.; Ryde, U.; Söderhjelm, P. Binding Affinities by Free-Energy Perturbation Using QM/MM with A Large QM System and Polarizable MM Model J. Comput. Chem. 2015, 36, 2114-2124 10.1002/jcc.24048
-
(2015)
J. Comput. Chem.
, vol.36
, pp. 2114-2124
-
-
Genheden, S.1
Ryde, U.2
Söderhjelm, P.3
-
379
-
-
84992301030
-
Converging Ligand-Binding Free Energies Obtained with Free-Energy Perturbations at the Quantum Mechanical Level
-
Olsson, M. A.; Söderhjelm, P.; Ryde, U. Converging Ligand-Binding Free Energies Obtained with Free-Energy Perturbations at the Quantum Mechanical Level J. Comput. Chem. 2016, 10.1002/jcc.24375
-
(2016)
J. Comput. Chem.
-
-
Olsson, M.A.1
Söderhjelm, P.2
Ryde, U.3
-
380
-
-
84921443655
-
Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation
-
Cave-Ayland, C.; Skylaris, C.-K.; Essex, J. W. Direct Validation of the Single Step Classical to Quantum Free Energy Perturbation J. Phys. Chem. B 2015, 119, 1017-1025 10.1021/jp506459v
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 1017-1025
-
-
Cave-Ayland, C.1
Skylaris, C.-K.2
Essex, J.W.3
-
381
-
-
0242364982
-
Calculation of free-energy differences from computer simulations of initial and final states
-
Hummer, G.; Szabo, A. Calculation of free-energy differences from computer simulations of initial and final states J. Chem. Phys. 1996, 105, 2004-2012 10.1063/1.472068
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 2004-2012
-
-
Hummer, G.1
Szabo, A.2
-
382
-
-
33745294923
-
QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction
-
Kästner, J.; Senn, H. M.; Thiel, S.; Otte, N.; Thiel, W. QM/MM Free-Energy Perturbation Compared to Thermodynamic Integration and Umbrella Sampling: Application to an Enzymatic Reaction J. Chem. Theory Comput. 2006, 2, 452-461 10.1021/ct050252w
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 452-461
-
-
Kästner, J.1
Senn, H.M.2
Thiel, S.3
Otte, N.4
Thiel, W.5
-
383
-
-
65249171993
-
Robust and Reliable Multilevel Minimization of the Kohn-Sham Energy
-
Jansík, B.; Høst, S.; Johansson, M. P.; Olsen, J.; Jørgensen, P.; Helgaker, T. Robust and Reliable Multilevel Minimization of the Kohn-Sham Energy J. Chem. Theory Comput. 2009, 5, 1027-1032 10.1021/ct800562h
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1027-1032
-
-
Jansík, B.1
Høst, S.2
Johansson, M.P.3
Olsen, J.4
Jørgensen, P.5
Helgaker, T.6
-
384
-
-
84884195343
-
Electrostatic Potential of Insulin: Exploring the Limitations of Density Functional Theory and Force Field Methods
-
Jakobsen, S.; Kristensen, K.; Jensen, F. Electrostatic Potential of Insulin: Exploring the Limitations of Density Functional Theory and Force Field Methods J. Chem. Theory Comput. 2013, 9, 3978-3985 10.1021/ct400452f
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3978-3985
-
-
Jakobsen, S.1
Kristensen, K.2
Jensen, F.3
-
385
-
-
33646104670
-
Peer Review: A Flawed Process at the Heart of Science and Journals
-
Smith, R. Peer Review: A Flawed Process at the Heart of Science and Journals J. R. Soc. Med. 2006, 99, 178-182 10.1258/jrsm.99.4.178
-
(2006)
J. R. Soc. Med.
, vol.99
, pp. 178-182
-
-
Smith, R.1
-
386
-
-
78649673341
-
Testing for the Presence of Positive-Outcome Bias in Peer Review. A Randomized Controlled Trial
-
Emerson, G. B.; Warme, W. J.; Wolf, F. M.; Heckman, J. D.; Brand, R. A.; Leopold, S. S. Testing for the Presence of Positive-Outcome Bias in Peer Review. A Randomized Controlled Trial Arch. Intern. Med. 2010, 170, 1934-1939 10.1001/archinternmed.2010.406
-
(2010)
Arch. Intern. Med.
, vol.170
, pp. 1934-1939
-
-
Emerson, G.B.1
Warme, W.J.2
Wolf, F.M.3
Heckman, J.D.4
Brand, R.A.5
Leopold, S.S.6
-
387
-
-
84893394271
-
Accuracy Assessment and Automation of Free Energy Calculations for Drug Design
-
Christ, C.; Fox, T. Accuracy Assessment and Automation of Free Energy Calculations for Drug Design J. Chem. Inf. Model. 2014, 54, 108-120 10.1021/ci4004199
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 108-120
-
-
Christ, C.1
Fox, T.2
-
388
-
-
84908225639
-
A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities
-
Mikulskis, P.; Genheden, S.; Ryde, U. A Large-Scale Test of Free-Energy Simulation Estimates of Protein-Ligand Binding Affinities J. Chem. Inf. Model. 2014, 54, 2794-2806 10.1021/ci5004027
-
(2014)
J. Chem. Inf. Model.
, vol.54
, pp. 2794-2806
-
-
Mikulskis, P.1
Genheden, S.2
Ryde, U.3
-
389
-
-
84923538660
-
Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
-
Wang, L.; Wu, Y.; Deng, Y.; Kim, B.; Pierce, L.; Krilov, G.; Lupyan, D.; Robinson, S.; Dahlgren, M. K.; Greenwood, J. et al. Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field J. Am. Chem. Soc. 2015, 137, 2695-2703 10.1021/ja512751q
-
(2015)
J. Am. Chem. Soc.
, vol.137
, pp. 2695-2703
-
-
Wang, L.1
Wu, Y.2
Deng, Y.3
Kim, B.4
Pierce, L.5
Krilov, G.6
Lupyan, D.7
Robinson, S.8
Dahlgren, M.K.9
Greenwood, J.10
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