-
1
-
-
1642357706
-
The Many Roles of Computation in Drug Discovery
-
DOI 10.1126/science.1096361
-
The Many Roles of Computation in Drug Discovery. WL Jorgensen, Science 2004 303 1813 (Pubitemid 38374866)
-
(2004)
Science
, vol.303
, Issue.5665
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
4
-
-
1642540577
-
Evaluation of Docking Performance: Comparative Data on Docking Algorithms
-
DOI 10.1021/jm0302997
-
Evaluation of Docking Performance: Comparative Data on Docking Algorithms. M Kontoyianni LM McClellan GS Sokol, J Med Chem 2004 47 558 565 10.1021/jm0302997 14736237 (Pubitemid 38129714)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.3
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
5
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
DOI 10.1021/jm0003992
-
Detailed Analysis of Scoring Functions for Virtual Screening. M Stahl M Rarey, J Med Chem 2001 44 1035 1042 10.1021/jm0003992 11297450 (Pubitemid 32852130)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.7
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
6
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
A Critical Assessment of Docking Programs and Scoring Functions. GL Warren CW Andrews A-M Capelli B Clarke J LaLonde MH Lambert M Lindvall N Nevins SF Semus S Senger,, et al. J Med Chem 2006 49 5912 5931 10.1021/jm050362n 17004707 (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, 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
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
7
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
19499576
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. O Trott AJ Olson, J Comput Chem 2010 31 455 461 19499576
-
(2010)
J Comput Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
8
-
-
0037008160
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
-
10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors. H Gohlke G Klebe, Angew Chem Int Edit 2002 41 2644 2676 10.1002/1521-3773(20020802)41:15<2644::AID- ANIE2644>3.0.CO;2-O
-
(2002)
Angew Chem Int Edit
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
9
-
-
0024578173
-
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems
-
10.1146/annurev.biophys.18.1.431
-
Free Energy Via Molecular Simulation: Applications to Chemical and Biomolecular Systems. DL Beveridge FM DiCapua, Annu Rev Biophys Bio 1989 18 431 492 10.1146/annurev.biophys.18.1.431
-
(1989)
Annu Rev Biophys Bio
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
10
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
Ligand binding affinity prediction by linear interaction energy methods. T Hansson J Marelius J qvist, J Comput Aided Mol Des 1998 12 27 35 10.1023/A:1007930623000 9570087 (Pubitemid 128513811)
-
(1998)
Journal of Computer-Aided Molecular Design
, vol.12
, Issue.1
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Aqvist, J.3
-
11
-
-
0342321950
-
Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
-
Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease. YY Sham Z-T Chu H Tao A Warshel, Proteins: Struct, Funct, Genet 2000 39 393 407 10.1002/(SICI)1097-0134(20000601)39:4<393::AID-PROT120>3.0.CO;2-H (Pubitemid 30414177)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.39
, Issue.4
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
-
12
-
-
0026596911
-
Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of free energies of binding of phosphorylcholine analogs to McPC603
-
10.1093/protein/5.3.215. 1409541
-
Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of free energies of binding of phosphorylcholine analogs to McPC603. FS Lee Z-T Chu MB Bolger A Warshel, Protein Eng 1992 5 215 228 10.1093/protein/5.3.215 1409541
-
(1992)
Protein Eng
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.-T.2
Bolger, M.B.3
Warshel, A.4
-
14
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Calculating Structures and Free Energies of Complex Molecules:? Combining Molecular Mechanics and Continuum Models. PA Kollman I Massova C Reyes B Kuhn S Huo L Chong M Lee T Lee Y Duan W Wang,, et al. Acc Chem Res 2000 33 889 897 10.1021/ar000033j 11123888 (Pubitemid 32056774)
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, 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
Donini, O.11
-
15
-
-
78751641417
-
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations
-
10.1209/0295-5075/91/37004
-
Protein-protein interactions from linear-scaling first-principles quantum-mechanical calculations. DJ Cole C-K Skylaris E Rajendra AR Venkitaraman MC Payne, 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
-
16
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
Validation and Use of the MM-PBSA Approach for Drug Discovery. B Kuhn P Gerber T Schulz-Gasch M Stahl, J Med Chem 2005 48 4040 4048 10.1021/jm049081q 15943477 (Pubitemid 40800612)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
17
-
-
76249112547
-
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA
-
19569205
-
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. G Rastelli AD Rio G Degliesposti M Sgobba, J Comput Chem 2010 31 797 810 19569205
-
(2010)
J Comput Chem
, vol.31
, pp. 797-810
-
-
Rastelli, G.1
Rio, A.D.2
Degliesposti, G.3
Sgobba, M.4
-
18
-
-
33645400172
-
A Multistep Approach to Structure-Based Drug Design:? Studying Ligand Binding at the Human Neutrophil Elastase
-
10.1021/jm0505720. 16539369
-
A Multistep Approach to Structure-Based Drug Design:? Studying Ligand Binding at the Human Neutrophil Elastase. T Steinbrecher DA Case A Labahn, J Med Chem 2006 49 1837 1844 10.1021/jm0505720 16539369
-
(2006)
J Med Chem
, vol.49
, pp. 1837-1844
-
-
Steinbrecher, T.1
Case, D.A.2
Labahn, A.3
-
19
-
-
84961980685
-
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
-
10.1021/jm000241h. 11020294
-
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models. B Kuhn PA Kollman, J Med Chem 2000 43 3786 3791 10.1021/jm000241h 11020294
-
(2000)
J Med Chem
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
20
-
-
0035846166
-
Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
-
DOI 10.1021/jm0100279
-
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System. DA Pearlman PS Charifson, J Med Chem 2001 44 3417 3423 10.1021/jm0100279 11585447 (Pubitemid 32947908)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.21
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
21
-
-
0029745052
-
Cation-π interactions in aromatics of biological and medicinal interest: Electrostatic potential surfaces as a useful qualitative guide
-
DOI 10.1073/pnas.93.20.10566
-
Cation-pi interactions in aromatics of biological and medicinal interest: electrostatic potential surfaces as a useful qualitative guide. P Mecozzi AP West Jr DA Dougherty, Proc Natl Acad Sci USA 1996 93 10566 10571 10.1073/pnas.93.20.10566 8855218 (Pubitemid 26333027)
-
(1996)
Proceedings of the National Academy of Sciences of the United States of America
, vol.93
, Issue.20
, pp. 10566-10571
-
-
Mecozzi, S.1
West Jr., A.P.2
Dougherty, D.A.3
-
22
-
-
0033578302
-
Cation- interactions in structural biology
-
10.1073/pnas.96.17.9459. 10449714
-
Cation- interactions in structural biology. JP Gallivan DA Dougherty, Proc Natl Acad Sci USA 1999 96 9459 9464 10.1073/pnas.96.17.9459 10449714
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9459-9464
-
-
Gallivan, J.P.1
Dougherty, D.A.2
-
23
-
-
0034703739
-
Origin of the Attraction and Directionality of the NH/p Interaction:? Comparison with OH/p and CH/p Interactions
-
10.1021/ja001901a
-
Origin of the Attraction and Directionality of the NH/p Interaction:? Comparison with OH/p and CH/p Interactions. S Tsuzuki K Honda T Uchimaru M Mikami K Tanabe, J Am Chem Soc 2000 122 11450 11458 10.1021/ja001901a
-
(2000)
J Am Chem Soc
, vol.122
, pp. 11450-11458
-
-
Tsuzuki, S.1
Honda, K.2
Uchimaru, T.3
Mikami, M.4
Tanabe, K.5
-
25
-
-
65249083371
-
On the Nature of Bonding in Lone Pairp-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations
-
10.1021/ct900036y
-
On the Nature of Bonding in Lone Pairp-Electron Complexes: CCSD(T)/Complete Basis Set Limit Calculations. J Ran P Hobza, J Chem Theory Comput 2009 5 1180 1185 10.1021/ct900036y
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 1180-1185
-
-
Ran, J.1
Hobza, P.2
-
26
-
-
58149491376
-
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems: A Users Manual and Examples
-
http://www.begdb.com
-
Quantum Chemical Benchmark Energy and Geometry Database for Molecular Clusters and Complex Molecular Systems: A Users Manual and Examples. J Rezc P Jurecka KE Riley J Cern H Valdes K Pluhckov K Berka T Rezc M Pitonk J Vondrek,, et al. Collect Czech Chem Commun 2008 73 1261 1270 http://www.begdb.com
-
(2008)
Collect Czech Chem Commun
, vol.73
, pp. 1261-1270
-
-
Rezc, J.1
Jurecka, P.2
Riley, K.E.3
Cern, J.4
Valdes, H.5
Pluhckov, K.6
Berka, K.7
Rezc, T.8
Pitonk, M.9
Vondrek, J.10
-
27
-
-
34548430376
-
The role of quantum mechanics in structure-based drug design
-
DOI 10.1016/j.drudis.2007.07.006, PII S1359644607002723
-
The role of quantum mechanics in structure-based drug design. K Raha MB Peters B Wang N Yu AM Wollacott LM Westerhoff KM Merz Jr, Drug Discov Today 2007 12 725 731 10.1016/j.drudis.2007.07.006 17826685 (Pubitemid 47364833)
-
(2007)
Drug Discovery Today
, vol.12
, Issue.17-18
, 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 Jr., K.M.7
-
28
-
-
0032833998
-
The role of polarization and charge transfer in the solvation of biomolecules
-
DOI 10.1021/ja9912325
-
The Role of Polarization and Charge Transfer in the Solvation of Biomolecules. A van der Vaart KM Merz Jr, J Am Chem Soc 1999 121 9182 9190 10.1021/ja9912325 (Pubitemid 29477385)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.39
, pp. 9182-9190
-
-
Van Der Vaart, A.1
Merz Jr., K.M.2
-
29
-
-
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
-
DOI 10.1021/jm048973n
-
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. K Raha KM Merz Jr, J Med Chem 2005 48 4558 4575 10.1021/jm048973n 15999994 (Pubitemid 40993417)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.14
, pp. 4558-4575
-
-
Raha, K.1
Merz Jr., K.M.2
-
30
-
-
0000721543
-
Fragment molecular orbital method: An approximate computational method for large molecules
-
PII S000926149900874X
-
Fragment molecular orbital method: an approximate computational method for large molecules. K Kitaura E Ikeo T Asada T Nakano M Uebayasi, Chem Phys Lett 1999 313 701 706 10.1016/S0009-2614(99)00874-X (Pubitemid 129556715)
-
(1999)
Chemical Physics Letters
, vol.313
, Issue.3-4
, pp. 701-706
-
-
Kitaura, K.1
Ikeo, E.2
Asada, T.3
Nakano, T.4
Uebayasi, M.5
-
31
-
-
26444446031
-
Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations
-
DOI 10.1002/prot.20578
-
Quantum computational analysis for drug resistance of HIV-1 reverse transcriptase to nevirapine through point mutations. X He Y Mei Y Xiang DW Zhang JZH Zhang, Proteins: Struct, Funct, Bioinf 2005 61 423 432 10.1002/prot.20578 (Pubitemid 41430485)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.61
, Issue.2
, pp. 423-432
-
-
He, X.1
Mei, Y.2
Xiang, Y.3
Zhang, D.W.4
Zhang, J.Z.H.5
-
32
-
-
33847088301
-
The Origin of Hydrogen Bonding. An Energy Decomposition Study
-
10.1021/ja00447a007
-
The Origin of Hydrogen Bonding. An Energy Decomposition Study. H Umeyama K Morokuma, J Am Chem Soc 1977 99 1316 1332 10.1021/ja00447a007
-
(1977)
J Am Chem Soc
, vol.99
, pp. 1316-1332
-
-
Umeyama, H.1
Morokuma, K.2
-
33
-
-
43949164521
-
Computation of charge-transfer energies by perturbation theory
-
10.1016/0009-2614(93)80058-W
-
Computation of charge-transfer energies by perturbation theory. AJ Stone, J Chem Phys Lett 1993 211 101 109 10.1016/0009-2614(93)80058-W
-
(1993)
J Chem Phys Lett
, vol.211
, pp. 101-109
-
-
Stone, A.J.1
-
34
-
-
0034227821
-
A general treatment of solvent effects based on screened Coulomb potentials
-
10.1021/jp993895e
-
A general treatment of solvent effects based on screened Coulomb potentials. SA Hassan, J Phys Chem B 2000 104 6478 6489 10.1021/jp993895e
-
(2000)
J Phys Chem B
, vol.104
, pp. 6478-6489
-
-
Hassan, S.A.1
-
35
-
-
0000121375
-
Divide and conquer interaction energy decomposition
-
10.1021/jp9844967
-
Divide and conquer interaction energy decomposition. A van der Vaart KM Merz Jr, J Phys Chem A 1999 103 3321 3329 10.1021/jp9844967
-
(1999)
J Phys Chem A
, vol.103
, pp. 3321-3329
-
-
Van Der Vaart, A.1
Merz Jr., K.M.2
-
36
-
-
33744470857
-
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
-
10.1039/b600027d. 16633685
-
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs. P Jurecka J poner J Cern P Hobza, Phys Chem Chem Phys 2006 8 1985 1993 10.1039/b600027d 16633685
-
(2006)
Phys Chem Chem Phys
, vol.8
, pp. 1985-1993
-
-
Jurecka, P.1
Poner, J.2
Cern, J.3
Hobza, P.4
-
37
-
-
36348986753
-
On the accurate reproduction of ab initio interaction energies between an enzyme and substrate
-
DOI 10.1016/j.cplett.2007.10.073, PII S0009261407014455
-
On the accurate reproduction of ab initio interaction energies between an enzyme and substrate. RPA Bettens AM Lee, Chem Phys Lett 2007 449 341 346 10.1016/j.cplett.2007.10.073 (Pubitemid 350160609)
-
(2007)
Chemical Physics Letters
, vol.449
, Issue.4-6
, pp. 341-346
-
-
Bettens, R.P.A.1
Lee, A.M.2
-
38
-
-
11144302905
-
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method
-
DOI 10.1002/jcc.20142
-
QMQSAR: Utilization of a semiempirical probe potential in a field-based QSAR method. S Dixon KM Merz Jr G Lauri JC Ianni, J Comput Chem 2005 26 23 34 10.1002/jcc.20142 15526326 (Pubitemid 40021620)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.1
, pp. 23-34
-
-
Dixon, S.1
Merz Jr., K.M.2
Lauri, G.3
Ianni, J.C.4
-
39
-
-
33646888111
-
Semiempirical Comparative Binding Energy Analysis (SE-COMBINE) of a Series of Trypsin Inhibitors
-
10.1021/ct050284j
-
Semiempirical Comparative Binding Energy Analysis (SE-COMBINE) of a Series of Trypsin Inhibitors. MB Peters KM Merz Jr, J Chem Theory Comput 2006 2 383 399 10.1021/ct050284j
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 383-399
-
-
Peters, M.B.1
Merz Jr., K.M.2
-
40
-
-
28044438176
-
Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein
-
DOI 10.1016/j.compbiolchem.2005.09.005, PII S147692710500099X
-
Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein. T Nemoto DG Fedorov M Uebayasi K Kanazawa K Kitaura Y Komeiji, Comput Biol Chem 2005 29 434 439 10.1016/j.compbiolchem.2005.09.005 16290169 (Pubitemid 41690443)
-
(2005)
Computational Biology and Chemistry
, vol.29
, Issue.6
, pp. 434-439
-
-
Nemoto, T.1
Fedorov, D.G.2
Uebayasi, M.3
Kanazawa, K.4
Kitaura, K.5
Komeiji, Y.6
-
41
-
-
1142279661
-
Quantum mechanical map for protein-ligand binding with application to -trypsin/benzamidine complex
-
10.1063/1.1639152. 15268233
-
Quantum mechanical map for protein-ligand binding with application to -trypsin/benzamidine complex. DW Zhang Y Xiang AM Gao JZH Zhang, J Chem Phys 2004 120 1145 1148 10.1063/1.1639152 15268233
-
(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
-
42
-
-
77952337364
-
Ligand Affinities Estimated by Quantum Chemical Calculations
-
Ligand Affinities Estimated by Quantum Chemical Calculations. P Söderhjelm J Kongsted U Ryde, J Chem Theory Comput 2010 6 1726 1737
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 1726-1737
-
-
Söderhjelm, P.1
Kongsted, J.2
Ryde, U.3
-
43
-
-
77953200013
-
Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches
-
10.1273/cbij.10.32
-
Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches. H Watanabe S Tanaka N Okimoto A Hasegawa M Taiji Y Tanida T Mitsui M Katsuyama H Fujitani, Chem-Bio Informatics Journal 2010 10 32 45 10.1273/cbij.10.32
-
(2010)
Chem-Bio Informatics Journal
, vol.10
, pp. 32-45
-
-
Watanabe, H.1
Tanaka, S.2
Okimoto, N.3
Hasegawa, A.4
Taiji, M.5
Tanida, Y.6
Mitsui, T.7
Katsuyama, M.8
Fujitani, H.9
-
44
-
-
54949153723
-
QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1 PR
-
QSAR Study of Cyclic Urea Type HIV-1 PR Inhibitors Using Ab Initio MO Calculation of Their Complex Structures with HIV-1 PR. T Yoshida K Yamagishi H Chuman, QSAR & Comb Sci 2008 27 694 703
-
(2008)
QSAR & Comb Sci
, vol.27
, pp. 694-703
-
-
Yoshida, T.1
Yamagishi, K.2
Chuman, H.3
-
45
-
-
65649135842
-
Novel Quantitative Structure-Activity Studies of HIV-1 Protease Inhibitors of the Cyclic Urea Type Using Descriptors Derived from Molecular Dynamics and Molecular Orbital Calculations
-
10.2174/157340909787580845
-
Novel Quantitative Structure-Activity Studies of HIV-1 Protease Inhibitors of the Cyclic Urea Type Using Descriptors Derived from Molecular Dynamics and Molecular Orbital Calculations. T Yoshida T Fujita H Chuman, Curr Comput Aided Drug Des 2009 5 38 55 10.2174/157340909787580845
-
(2009)
Curr Comput Aided Drug des
, vol.5
, pp. 38-55
-
-
Yoshida, T.1
Fujita, T.2
Chuman, H.3
-
46
-
-
77952772108
-
Correlation analyses on binding affinity of Substituted benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on their Complex structures
-
10.1021/ci100068w. 20415451
-
Correlation analyses on binding affinity of Substituted benzenesulfonamides with carbonic anhydrase using ab initio MO calculations on their Complex structures. T Yoshida Y Munei S Hitaoka H Chuman, J Chem Inf Model 2010 50 850 860 10.1021/ci100068w 20415451
-
(2010)
J Chem Inf Model
, vol.50
, pp. 850-860
-
-
Yoshida, T.1
Munei, Y.2
Hitaoka, S.3
Chuman, H.4
-
48
-
-
50249083873
-
Identification of N-(4-Piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design
-
10.1021/jm800382h. 18656911
-
Identification of N-(4-Piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H- pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design PG Wyatt AJ Woodhead V Berdini JA Boulstridge MG Carr DM Cross DJ Davis LA Devine TR Early RE Feltell,, et al. J Med Chem 2008 51 4986 4999 10.1021/jm800382h 18656911
-
(2008)
J Med Chem
, vol.51
, pp. 4986-4999
-
-
Wyatt, P.G.1
Woodhead, A.J.2
Berdini, V.3
Boulstridge, J.A.4
Carr, M.G.5
Cross, D.M.6
Davis, D.J.7
Devine, L.A.8
Early, T.R.9
Feltell, R.E.10
-
50
-
-
0342645331
-
-
1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7, Chemical Computing Group Inc
-
MOE (The Molecular Operating Environment). (2009.10). 1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7, Chemical Computing Group Inc 2009
-
(2009)
MOE (The Molecular Operating Environment). (2009.10)
-
-
-
51
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
-
10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. A Jakalian BL Bush DB Jack CI Bayly, J Comput Chem 2000 21 132 146 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
-
(2000)
J Comput Chem
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
52
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. A Jakalian DB Jack CI Bayly, J Comput Chem 2002 23 1623 1641 10.1002/jcc.10128 12395429 (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
53
-
-
33748790698
-
Facio: New Computational Chemistry Environment for PC GAMESS
-
10.2477/jccj.4.25
-
Facio: New Computational Chemistry Environment for PC GAMESS. M Suenaga, J Comput Chem Jpn 2005 4 25 32 10.2477/jccj.4.25
-
(2005)
J Comput Chem Jpn
, vol.4
, pp. 25-32
-
-
Suenaga, M.1
-
54
-
-
67650754298
-
Development of GUI for GAMESS/FMO Calculation
-
10.2477/jccj.H1920
-
Development of GUI for GAMESS/FMO Calculation. M Suenaga, J Comput Chem Jpn 2008 7 33 53 10.2477/jccj.H1920
-
(2008)
J Comput Chem Jpn
, vol.7
, pp. 33-53
-
-
Suenaga, M.1
-
55
-
-
0000170061
-
Pair interaction molecular orbital method: An approximate computational method for molecular interactions
-
PII S0009261499009379
-
Pair interaction molecular orbital method: an approximate computational method for molecular interactions. K Kitaura T Sawai T Asada T Nakano M Uebayasi, Chem Phys Lett 1999 312 319 324 10.1016/S0009-2614(99)00937-9 (Pubitemid 129556608)
-
(1999)
Chemical Physics Letters
, vol.312
, Issue.2-4
, pp. 319-324
-
-
Kitaura, K.1
Sawai, T.2
Asada, T.3
Nakano, T.4
Uebayasi, M.5
-
57
-
-
0037122848
-
Fragment molecular orbital method: Use of approximate electrostatic potential
-
10.1016/S0009-2614(01)01416-6
-
Fragment molecular orbital method: use of approximate electrostatic potential. T Nakano T Kaminuma T Sato K Fukuzawa Y Akiyama M Uebayasi K Kitaura, Chem Phys Lett 2002 351 475 480 10.1016/S0009-2614(01)01416-6
-
(2002)
Chem Phys Lett
, vol.351
, pp. 475-480
-
-
Nakano, T.1
Kaminuma, T.2
Sato, T.3
Fukuzawa, K.4
Akiyama, Y.5
Uebayasi, M.6
Kitaura, K.7
-
58
-
-
84893169025
-
General Atomic and Molecular Electronic Structure System
-
10.1002/jcc.540141112
-
General Atomic and Molecular Electronic Structure System. MW Schmidt KK Baldridge JA Boatz ST Elbert MS Gordon JH Jensen S Koseki N Matsunaga KA Nguyen SJ Su,, et al. J Comput Chem 1993 14 1347 1363 10.1002/jcc.540141112
-
(1993)
J Comput Chem
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.J.10
-
60
-
-
84885102778
-
Advances in electronic structure theory: GAMESS a decade later
-
Amsterdam: Elsevier, Dykstra CE, Frenking G, Kim KS, Scuseria GE
-
Advances in electronic structure theory: GAMESS a decade later. MS Gordon MW Schmidt, Theory and Applications of Computational Chemistry, the first forty years Amsterdam: Elsevier, Dykstra CE, Frenking G, Kim KS, Scuseria GE, 2005 1167 1189 full-text
-
(2005)
Theory and Applications of Computational Chemistry, the First Forty Years
, pp. 1167-1189
-
-
Gordon, M.S.1
Schmidt, M.W.2
-
61
-
-
34548779129
-
Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method
-
10.1016/j.bpc.2007.06.011
-
Visualization analysis of inter-fragment interaction energies of CRP-cAMP-DNA complex based on the fragment molecular orbital method. I Kurisakia K Fukuzawab Y Komeijic Y Mochizukic T Nakanoc J Imadag A Chmielewskig SM Rothsteing H Watanabea S Tanakaa, Biophys Chem 2010 130 1 9 10.1016/j.bpc.2007. 06.011
-
(2010)
Biophys Chem
, vol.130
, pp. 1-9
-
-
Kurisakia, I.1
Fukuzawab, K.2
Komeijic, Y.3
Mochizukic, Y.4
Nakanoc, T.5
Imadag, J.6
Chmielewskig, A.7
Rothsteing, S.M.8
Watanabea, H.9
Tanakaa, S.10
-
62
-
-
33244464010
-
VISCANA: Visualized cluster analysis of protein - Ligand interaction based on the ab initio fragment molecular orbital method for virtual ligand screening
-
DOI 10.1021/ci050262q
-
VISCANA: Visualized Cluster Analysis of Protein-Ligand Interaction Based on the ab Initio Fragment Molecular Orbital Method for Virtual Ligand Screening. S Amari M Aizawa J Zhang K Fukuzawa Y Mochizuki Y Iwasawa K Nakata H Chuman T Nakano, J Chem Inf Model 2006 46 221 230 10.1021/ci050262q 16426058 (Pubitemid 43282117)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.1
, 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
-
63
-
-
33646586407
-
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study
-
DOI 10.1002/jcc.20399
-
Intra- and intermolecular interactions between cyclic-AMP receptor protein and DNA: Ab initio fragment molecular orbital study. K Fukuzawa Y Komeiji Y Mochizuki A Kato T Nakano S Tanaka, J Comput Chem 2006 27 948 960 10.1002/jcc.20399 16586530 (Pubitemid 43723217)
-
(2006)
Journal of Computational Chemistry
, vol.27
, Issue.8
, pp. 948-960
-
-
Fukuzawa, K.1
Komeiji, Y.2
Mochizuki, Y.3
Kato, A.4
Nakano, T.5
Tanaka, S.6
-
64
-
-
33846595219
-
Pair interaction energy decomposition analysis
-
DOI 10.1002/jcc.20496
-
Pair interaction energy decomposition analysis. DG Fedorov K Kitaura, J Comput Chem 2007 28 222 237 10.1002/jcc.20496 17109433 (Pubitemid 46180489)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.1
, pp. 222-237
-
-
Fedorov, D.G.1
Kitaura, K.2
-
65
-
-
84987133653
-
A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation
-
10.1002/qua.560100211
-
A new energy decomposition scheme for molecular interactions within the Hartree-Fock approximation. K Kitaura K Morokuma, Int J Quantum Chem 1976 10 325 340 10.1002/qua.560100211
-
(1976)
Int J Quantum Chem
, vol.10
, pp. 325-340
-
-
Kitaura, K.1
Morokuma, K.2
-
66
-
-
0036722785
-
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
-
DOI 10.1002/jcc.10112
-
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? SM Schwarzl TB Tschopp JC Smith S Fischer, J Comput Chem 2002 23 1143 1149 10.1002/jcc.10112 12116383 (Pubitemid 34854445)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.12
, pp. 1143-1149
-
-
Schwarzl, S.M.1
Tschopp, T.B.2
Smith, J.C.3
Fischer, S.4
-
67
-
-
0036821028
-
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
-
DOI 10.1023/A:1022446720849
-
The consequences of translational and rotational entropy lost by small molecules on binding to proteins. CW Murray ML Verdonk, J Comput Aided Mol Des 2002 16 741 753 10.1023/A:1022446720849 12650591 (Pubitemid 36336183)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.10
, pp. 741-753
-
-
Murray, C.W.1
Verdonk, M.L.2
-
68
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
DOI 10.1021/jm060763i
-
Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein-Ligand Binding. J Tirado-Rives WL Jorgensen, J Med Chem 2006 49 5880 5884 10.1021/jm060763i 17004703 (Pubitemid 44484934)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
69
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. MD Eldridge CW Murray TR Auton GV Paolini RP Mee, J Comput Aided Mol Des 1997 11 425 445 10.1023/A:1007996124545 9385547 (Pubitemid 127505895)
-
(1997)
Journal of Computer-Aided Molecular Design
, vol.11
, Issue.5
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
70
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
7964925
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. H-J Böhm, J Comput Aided Mol Des 1994 8 243 256 7964925
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 243-256
-
-
Böhm, H.-J.1
-
71
-
-
0037142298
-
SMall Molecule Growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
-
DOI 10.1021/jm0105833
-
SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein-Ligand Interactions. AV Ishchenko EI Shakhnovich, J Med Chem 2002 45 2770 2780 10.1021/jm0105833 12061879 (Pubitemid 34627647)
-
(2002)
Journal of Medicinal Chemistry
, vol.45
, Issue.13
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich, E.I.2
-
72
-
-
0942276314
-
A Quantum Mechanics-Based Scoring Function: Study of Zinc Ion-Mediated Ligand Binding
-
DOI 10.1021/ja038496i
-
A Quantum Mechanics-Based Scoring Function:? Study of Zinc Ion-Mediated Ligand Binding. K Raha KM Merz Jr, J Am Chem Soc 2004 126 1020 1021 10.1021/ja038496i 14746460 (Pubitemid 38140722)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.4
, pp. 1020-1021
-
-
Raha, K.1
Merz Jr., K.M.2
-
73
-
-
77957954013
-
Mixed Quantum Mechanics/Molecular Mechanics Scoring Function to Predict Protein-Ligand Binding Affinity
-
10.1021/ct100315g. 21221417
-
Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein-Ligand Binding Affinity. SA Hayik R Dunbrack Jr KM Merz Jr, J Chem Theory Comput 2010 6 3079 3091 10.1021/ct100315g 21221417
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 3079-3091
-
-
Hayik, S.A.1
Dunbrack Jr., R.2
Merz Jr., K.M.3
-
74
-
-
0000598486
-
Using a Convenient, Quantitative Model for Torsional Entropy to Establish Qualitative Trends for Molecular Processes That Restrict Conformational Freedom
-
Using a Convenient, Quantitative Model for Torsional Entropy To Establish Qualitative Trends for Molecular Processes That Restrict Conformational Freedom. M Mammen EI Shakhnovich GM Whitesides, J Org Chem 1998 63 3168 3175 10.1021/jo970943n (Pubitemid 128500459)
-
(1998)
Journal of Organic Chemistry
, vol.63
, Issue.10
, pp. 3168-3175
-
-
Mammen, M.1
Shakhnovich, E.I.2
Whitesides, G.M.3
-
75
-
-
0011930746
-
Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area
-
10.1021/j100663a023
-
Theory of hydrophobic bonding. II. Correlation of hydrocarbon solubility in water with solvent cavity surface area. RB Hermann, J Phys Chem 1972 76 2754 2759 10.1021/j100663a023
-
(1972)
J Phys Chem
, vol.76
, pp. 2754-2759
-
-
Hermann, R.B.1
-
76
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical applications
-
10.1021/j100108a002
-
Macroscopic models of aqueous solutions: biological and chemical applications. B Honig K Sharp AS Yang, J Phys Chem 1993 97 1101 1109 10.1021/j100108a002
-
(1993)
J Phys Chem
, vol.97
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.S.3
-
77
-
-
84884674606
-
SIMCAP (11.0.0.0)
-
Umeå, Sweden, Umetrics AB
-
SIMCAP (11.0.0.0). Box 7960, SE90719 Umeå, Sweden, Umetrics AB 2005
-
(2005)
Box 7960, SE90719
-
-
-
79
-
-
77958551314
-
Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures
-
10.1021/ci100225b. 20863103
-
Correlation Analyses on Binding Affinity of Sialic Acid Analogues with Influenza Virus Neuraminidase-1 Using ab Initio MO Calculations on Their Complex Structures. S Hitaoka M Harada T Yoshida H Chuman, J Chem Inf Model 2010 50 1796 1805 10.1021/ci100225b 20863103
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1796-1805
-
-
Hitaoka, S.1
Harada, M.2
Yoshida, T.3
Chuman, H.4
-
80
-
-
2342586724
-
Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding
-
DOI 10.1021/jm030563w
-
Conformational Analysis of Drug-Like Molecules Bound to Proteins:? An Extensive Study of Ligand Reorganization upon Binding. E Perola PS Charifson, J Med Chem 2004 47 2499 2510 10.1021/jm030563w 15115393 (Pubitemid 38580088)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.10
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.S.2
-
81
-
-
34347224684
-
Calculation of protein-ligand binding affinities
-
DOI 10.1146/annurev.biophys.36.040306.132550
-
Calculation of Protein-Ligand Binding Affinities. MK Gilson H-X Zhou, Annu Rev Biophys Biomol Struct 2007 36 21 42 10.1146/annurev.biophys.36.040306. 132550 17201676 (Pubitemid 46998108)
-
(2007)
Annual Review of Biophysics and Biomolecular Structure
, vol.36
, pp. 21-42
-
-
Gilson, M.K.1
Zhou, H.-X.2
-
82
-
-
70350349240
-
A Study of CDK2 Inhibitors Using a Novel 3D-QSAR Method Exploiting Receptor Flexibility
-
A Study of CDK2 Inhibitors Using a Novel 3D-QSAR Method Exploiting Receptor Flexibility. MP Mazanetz IM Withers CA Laughton PM Fischer, QSAR & Comb Sci 2009 28 878 884
-
(2009)
QSAR & Comb Sci
, vol.28
, pp. 878-884
-
-
Mazanetz, M.P.1
Withers, I.M.2
Laughton, C.A.3
Fischer, P.M.4
-
83
-
-
52149095458
-
The effect of MM polarization on the QM/MM transition state stabilization: Application to chorismate mutase
-
10.1080/00268970802077850
-
The effect of MM polarization on the QM/MM transition state stabilization: application to chorismate mutase. CJR Illingworth KE Parkes CR Snell S Marti V Moliner CA Reynolds, Mol Phys 2008 106 1511 1515 10.1080/00268970802077850
-
(2008)
Mol Phys
, vol.106
, pp. 1511-1515
-
-
Illingworth, C.J.R.1
Parkes, K.E.2
Snell, C.R.3
Marti, S.4
Moliner, V.5
Reynolds, C.A.6
-
84
-
-
34250745809
-
Compensating enthalpic and entropic changes hinder binding affinity optimization
-
DOI 10.1111/j.1747-0285.2007.00519.x
-
Compensating Enthalpic and Entropic Changes Hinder Binding Affinity Optimization. V Lafont AA Armstrong H Ohtaka Y Kiso LM Amzel E Freire, Chem Biol Drug Des 2007 69 413 422 10.1111/j.1747-0285.2007.00519.x 17581235 (Pubitemid 46955533)
-
(2007)
Chemical Biology and Drug Design
, vol.69
, Issue.6
, pp. 413-422
-
-
Lafont, V.1
Armstrong, A.A.2
Ohtaka, H.3
Kiso, Y.4
Mario Amzel, L.5
Freire, E.6
-
85
-
-
52049123291
-
Do enthalpy and entropy distinguish first in class from best in class?
-
10.1016/j.drudis.2008.07.005. 18703160
-
Do enthalpy and entropy distinguish first in class from best in class? E Freire, Drug Discov Today 2008 13 869 874 10.1016/j.drudis.2008.07.005 18703160
-
(2008)
Drug Discov Today
, vol.13
, pp. 869-874
-
-
Freire, E.1
-
87
-
-
33646565044
-
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)
-
DOI 10.1002/jcc.20406
-
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). DG Fedorov K Kitaura H Li JH Jensen MS Gordon, J Comput Chem 2006 27 976 985 10.1002/jcc.20406 16604514 (Pubitemid 43723220)
-
(2006)
Journal of Computational Chemistry
, vol.27
, Issue.8
, pp. 976-985
-
-
Fedorov, D.G.1
Kitaura, K.2
Li, H.3
Jensen, J.H.4
Gordon, M.S.5
-
88
-
-
78649965861
-
Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation
-
10.1016/j.cplett.2010.10.017
-
Incorporation of solvation effects into the fragment molecular orbital calculations with the Poisson-Boltzmann equation. H Watanabe Y Okiyama T Nakano S Tanaka, 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
|