-
1
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
DOI 10.1021/jm030489h
-
Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessing Scoring Functions for Protein-Ligand Interactions J. Med. Chem. 2004, 47, 3032-3047 (Pubitemid 38702700)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.12
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Brooks III, C.L.5
-
2
-
-
10044294023
-
An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes
-
Wang, R.; Lu, Y.; Fang, X.; Wang, S. An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes J. Chem. Inf. Comput. Sci. 2004, 44, 2114-2125
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
3
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
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.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931 (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
-
4
-
-
0037008160
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
-
Gohlke, H.; Klebe, G. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors Angew. Chem., Int. Ed. 2002, 41, 2644-2676
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
5
-
-
33846863158
-
Solvated Interaction Energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space
-
DOI 10.1021/ci600406v
-
Naim, M.; Bhat, S.; Rankin, K. N.; Dennis, S.; Chowdhury, S. F.; Siddiqi, I.; Drabik, P.; Sulea, T.; Bayly, C. I.; Jakalian, A.; Purisima, E. O. Solvated Interaction Energy (SIE) for Scoring Protein-Ligand Binding Affinities. 1. Exploring the Parameter Space J. Chem. Inf. Model. 2007, 47, 122-133 (Pubitemid 46225568)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.1
, pp. 122-133
-
-
Naim, M.1
Bhat, S.2
Rankin, K.N.3
Dennis, S.4
Chowdhury, S.F.5
Siddiqi, I.6
Drabik, P.7
Sulea, T.8
Bayly, C.I.9
Jakalian, A.10
Purisima, E.O.11
-
6
-
-
44149094011
-
Molecular Dynamics-Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex
-
Cui, Q.; Sulea, T.; Schrag, J. D.; Munger, C.; Hung, M. N.; Naim, M.; Cygler, M.; Purisima, E. O. Molecular Dynamics-Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex J. Mol. Biol. 2008, 379, 787-802
-
(2008)
J. Mol. Biol.
, vol.379
, pp. 787-802
-
-
Cui, Q.1
Sulea, T.2
Schrag, J.D.3
Munger, C.4
Hung, M.N.5
Naim, M.6
Cygler, M.7
Purisima, E.O.8
-
7
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897 (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
-
8
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and Use of the MM-PBSA Approach for Drug Discovery J. Med. Chem. 2005, 48, 4040-4048 (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
-
9
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke, H.; Kiel, C.; Case, D. A. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf J. Comput. Chem. 2004, 25, 238-250
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Kiel, C.2
Case, D.A.3
-
10
-
-
0035665229
-
The linear interaction energy method for predicting ligand binding free energies
-
Aqvist, J.; Marelius, J. The linear interaction energy method for predicting ligand binding free energies Comb. Chem. High Throughput Screening 2001, 4, 613-626 (Pubitemid 34003156)
-
(2001)
Combinatorial Chemistry and High Throughput Screening
, vol.4
, Issue.8
, pp. 613-626
-
-
Aqvist, J.1
Marelius, J.2
-
11
-
-
0036280661
-
Ligand Binding Affinities from MD Simulations
-
Aqvist, J.; Luzhkov, V. B.; Brandsdal, B. O. Ligand Binding Affinities from MD Simulations Acc. Chem. Res. 2002, 35, 358-365
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 358-365
-
-
Aqvist, J.1
Luzhkov, V.B.2
Brandsdal, B.O.3
-
12
-
-
0037693081
-
On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations
-
Rankin, K. N.; Sulea, T.; Purisima, E. O. On the transferability of hydration-parametrized continuum electrostatics models to solvated binding calculations J. Comput. Chem. 2003, 25, 954-962
-
(2003)
J. Comput. Chem.
, vol.25
, pp. 954-962
-
-
Rankin, K.N.1
Sulea, T.2
Purisima, E.O.3
-
13
-
-
16344395749
-
Calculation of cyclodextrin binding affinities: Energy, entropy, and implications for drug design
-
DOI 10.1529/biophysj.104.049494
-
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 (Pubitemid 40468563)
-
(2004)
Biophysical Journal
, vol.87
, Issue.5
, pp. 3035-3049
-
-
Chen, W.1
Chang, C.-E.2
Gilson, M.K.3
-
14
-
-
5644287368
-
Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm
-
Chang, C. E.; Gilson, M. K. Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm J. Am. Chem. Soc. 2004, 126, 13156-13164 (Pubitemid 39372346)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.40
, pp. 13156-13164
-
-
Chang, C.-E.1
Gilson, M.K.2
-
15
-
-
84863101746
-
The solvated interaction energy (SIE) method for scoring binding affinities
-
Baron, R. Humana Press: USA (Springer publishing group): submitted for publication
-
Sulea, T.; Purisima, E. O. The solvated interaction energy (SIE) method for scoring binding affinities. In Methods in Molecular Biology, Computer-Aided Drug Design; Baron, R., Ed.; Humana Press: USA (Springer publishing group): 2011, submitted for publication.
-
(2011)
Methods in Molecular Biology, Computer-Aided Drug Design
-
-
Sulea, T.1
Purisima, E.O.2
-
16
-
-
65249155929
-
Blind Challenge for Computational Solvation Free Energies: Introduction and Overview
-
Guthrie, J. P. A Blind Challenge for Computational Solvation Free Energies: Introduction and Overview J. Phys. Chem. B 2009, 113, 4501-4507
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4501-4507
-
-
Guthrie, J.P.A.1
-
17
-
-
77953325344
-
The SAMPL2 blind prediction challenge: Introduction and overview
-
Geballe, M.; Skillman, A.; Nicholls, A.; Guthrie, J.; Taylor, P. The SAMPL2 blind prediction challenge: introduction and overview J. Comput.-Aided Mol. Des. 2010, 24, 259-279
-
(2010)
J. Comput.-Aided Mol. Des.
, vol.24
, pp. 259-279
-
-
Geballe, M.1
Skillman, A.2
Nicholls, A.3
Guthrie, J.4
Taylor, P.5
-
18
-
-
77953321666
-
SAMPL2 challenge: Prediction of solvation energies and tautomer ratios
-
Skillman, A.; Geballe, M.; Nicholls, A. SAMPL2 challenge: prediction of solvation energies and tautomer ratios J. Comput.-Aided Mol. Des. 2010, 24 (4) 257-258
-
(2010)
J. Comput.-Aided Mol. Des.
, vol.24
, Issue.4
, pp. 257-258
-
-
Skillman, A.1
Geballe, M.2
Nicholls, A.3
-
19
-
-
80053306915
-
SAMPL1 at first glance
-
Santa Fe, NM, March 19, (accessed July 11, 2011)
-
Skillman, G. SAMPL1 at first glance. CUP-IX Meeting, Santa Fe, NM, March 19, 2008, http://eyesopen.com/2008-cup-presentations/CUP9-Skillman.pdf (accessed July 11, 2011).
-
(2008)
CUP-IX Meeting
-
-
Skillman, G.1
-
20
-
-
70350501157
-
Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method
-
Wang, Y. T.; Su, Z. Y.; Hsieh, C. H.; Chen, C. L. Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method J. Chem. Inf. Model. 2009, 49, 2369-2375
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2369-2375
-
-
Wang, Y.T.1
Su, Z.Y.2
Hsieh, C.H.3
Chen, C.L.4
-
21
-
-
77955769458
-
Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations
-
Mishra, N. K.; Kriz, Z.; Wimmerova, M.; Koca, J. Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations Carbohydr. Res. 2010, 345, 1432-1441
-
(2010)
Carbohydr. Res.
, vol.345
, pp. 1432-1441
-
-
Mishra, N.K.1
Kriz, Z.2
Wimmerova, M.3
Koca, J.4
-
22
-
-
53549105246
-
Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation
-
Rodriguez-Granillo, A.; Sedlak, E.; Wittung-Stafshede, P. Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation J. Mol. Biol. 2008, 383, 1097-1111
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 1097-1111
-
-
Rodriguez-Granillo, A.1
Sedlak, E.2
Wittung-Stafshede, P.3
-
23
-
-
77955557080
-
Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields
-
Wei, C.; Mei, Y.; Zhang, D. Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields Chem. Phys. Lett. 2010, 495, 121-124
-
(2010)
Chem. Phys. Lett.
, vol.495
, pp. 121-124
-
-
Wei, C.1
Mei, Y.2
Zhang, D.3
-
24
-
-
33947718470
-
The S2 subsites of cathepsins K and L and their contribution to collagen degradation
-
DOI 10.1110/ps.062666607
-
Lecaille, F.; Chowdhury, S.; Purisima, E.; Bromme, D.; Lalmanach, G. The S2 subsites of cathepsins K and L and their contribution to collagen degradation Protein Sci. 2007, 16, 662-670 (Pubitemid 46506995)
-
(2007)
Protein Science
, vol.16
, Issue.4
, pp. 662-670
-
-
Lecaille, F.1
Chowdhury, S.2
Purisima, E.3
Bromme, D.4
Lalmanach, G.5
-
25
-
-
37649023004
-
Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis
-
Nguyen, M.; Marcellus, R. C.; Roulston, A.; Watson, M.; Serfass, L.; Murthy Madiraju, S. R.; Goulet, D.; Viallet, J.; Belec, L.; Billot, X.; Acoca, S.; Purisima, E.; Wiegmans, A.; Cluse, L.; Johnstone, R. W.; Beauparlant, P.; Shore, G. C. Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 19512-19517
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 19512-19517
-
-
Nguyen, M.1
Marcellus, R.C.2
Roulston, A.3
Watson, M.4
Serfass, L.5
Murthy Madiraju, S.R.6
Goulet, D.7
Viallet, J.8
Belec, L.9
Billot, X.10
Acoca, S.11
Purisima, E.12
Wiegmans, A.13
Cluse, L.14
Johnstone, R.W.15
Beauparlant, P.16
Shore, G.C.17
-
26
-
-
77950037970
-
Structure-activity relationship of novel DAPK inhibitors identified by structure-based virtual screening
-
Okamoto, M.; Takayama, K.; Shimizu, T.; Muroya, A.; Furuya, T. Structure-activity relationship of novel DAPK inhibitors identified by structure-based virtual screening Bioorg. Med. Chem. 2010, 18, 2728-2734
-
(2010)
Bioorg. Med. Chem.
, vol.18
, pp. 2728-2734
-
-
Okamoto, M.1
Takayama, K.2
Shimizu, T.3
Muroya, A.4
Furuya, T.5
-
27
-
-
78650150026
-
Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives
-
Yang, B.; Hamza, A.; Chen, G.; Wang, Y.; Zhan, C. G. Computational Determination of Binding Structures and Free Energies of Phosphodiesterase-2 with Benzo[1,4]diazepin-2-one Derivatives J. Phys. Chem. B 2010, 114, 16020-16028
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 16020-16028
-
-
Yang, B.1
Hamza, A.2
Chen, G.3
Wang, Y.4
Zhan, C.G.5
-
28
-
-
67349148279
-
Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. in silico and in vitro mutagenesis
-
Wimmerova, M.; Mishra, N.; Pokorna, M.; Koca, J. Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis J. Mol. Model. 2009, 15, 673-679
-
(2009)
J. Mol. Model.
, vol.15
, pp. 673-679
-
-
Wimmerova, M.1
Mishra, N.2
Pokorna, M.3
Koca, J.4
-
29
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
30
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
31
-
-
0000667030
-
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation J. Am. Chem. Soc. 1993, 115, 9620-9631
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollman, P.A.4
-
32
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
-
Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method J. Comput. Chem. 2000, 21, 132-146
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
33
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23, 1623-1641 (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
-
34
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Modell. 2006, 25, 247-260 (Pubitemid 44363172)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.2
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
35
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
36
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
Case, D. A.; Cheatham, T. E.; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26, 1668-1688 (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
37
-
-
84986456126
-
A Simple yet Accurate Boundary Element Method for Continuum Dielectric Calculations
-
Purisima, E. O.; Nilar, S. H. A Simple yet Accurate Boundary Element Method for Continuum Dielectric Calculations J. Comput. Chem. 1995, 16, 681-689
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 681-689
-
-
Purisima, E.O.1
Nilar, S.H.2
-
38
-
-
0005652597
-
Fast summation boundary element method for calculating solvation free energies of macromolecules
-
Purisima, E. O. Fast summation boundary element method for calculating solvation free energies of macromolecules J. Comput. Chem. 1998, 19, 1494-1504 (Pubitemid 128592640)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.13
, pp. 1494-1504
-
-
Purisima, E.O.1
-
39
-
-
0031619647
-
A new tetrahedral tesselation scheme for isosurface generation
-
PII S009784939700085X
-
Chan, S. L.; Purisima, E. O. A new tetrahedral tesselation scheme for isosurface generation Comput. Graphics 1998, 22, 83-90 (Pubitemid 128412907)
-
(1998)
Computers and Graphics (Pergamon)
, vol.22
, Issue.1
, pp. 83-90
-
-
Chan, S.L.1
Purisima, E.O.2
-
40
-
-
84961983475
-
Molecular surface generation using marching tetrahedra
-
Chan, S. L.; Purisima, E. O. Molecular surface generation using marching tetrahedra J. Comput. Chem. 1998, 19, 1268-1277 (Pubitemid 128616669)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.11
, pp. 1268-1277
-
-
Chan, S.L.1
Purisima, E.O.2
-
41
-
-
30344480798
-
Molecular surface generation using a variable-radius solvent probe
-
DOI 10.1002/prot.20682
-
Bhat, S.; Purisima, E. O. Molecular surface generation using a variable-radius solvent probe Proteins 2006, 62, 244-261 (Pubitemid 43063022)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.62
, Issue.1
, pp. 244-261
-
-
Bhat, S.1
Purisima, E.O.2
-
42
-
-
58049201323
-
-
University of California: San Francisco, CA
-
Case, D. A; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. AMBER 10; University of California: San Francisco, CA, 2008.
-
(2008)
AMBER 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
43
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
44
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 2006, 65, 712-725 (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
45
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21, 1049-1074
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
46
-
-
33846823909
-
Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: An N.log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
47
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
48
-
-
20644449471
-
Modification of the Generalized Born Model Suitable for Macromolecules
-
Onufriev, A.; Bashford, D.; Case, D. A. Modification of the Generalized Born Model Suitable for Macromolecules J. Phys. Chem. B 2000, 104, 3712-3720
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 3712-3720
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
49
-
-
33751385054
-
Macroscopic models of aqueous solutions: Biological and chemical applications
-
Honig, B.; Sharp, K.; Yang, A. S. Macroscopic models of aqueous solutions: biological and chemical applications J. Phys. Chem. 1993, 97, 1101-1109
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 1101-1109
-
-
Honig, B.1
Sharp, K.2
Yang, A.S.3
-
50
-
-
32844457567
-
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models J. Phys. Chem. 1994, 98, 1978-1988
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
52
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7, 385-391 (Pubitemid 24063137)
-
(1994)
Protein Engineering
, vol.7
, Issue.3
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
53
-
-
0026596911
-
Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
-
Lee, F. S.; Chu, Z. T.; Bolger, M. B.; Warshel, A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603 Protein Eng. 1992, 5, 215-228
-
(1992)
Protein Eng.
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.T.2
Bolger, M.B.3
Warshel, A.4
-
54
-
-
36649023306
-
Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies
-
Almlof, M.; Carlsson, J.; Aqvist, J. Improving the Accuracy of the Linear Interaction Energy Method for Solvation Free Energies J. Chem. Theory Comput. 2007, 3, 2162-2175
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2162-2175
-
-
Almlof, M.1
Carlsson, J.2
Aqvist, J.3
-
55
-
-
77952388331
-
Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE)
-
Sulea, T.; Corbeil, C. R.; Purisima, E. O. Rapid Prediction of Solvation Free Energy. 1. An Extensive Test of Linear Interaction Energy (LIE) J. Chem. Theory Comput. 2010, 6, 1608-1621
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1608-1621
-
-
Sulea, T.1
Corbeil, C.R.2
Purisima, E.O.3
-
56
-
-
0028157224
-
Inhibition and catalysis of carbonic anhydrase - Recent crystallographic analyses
-
Liljas, A.; Hakansson, K.; Jonsson, B. H.; Xue, Y. Inhibition and catalysis of carbonic anhydrase. Recent crystallographic analyses Eur. J. Biochem. 1994, 219, 1-10 (Pubitemid 24053612)
-
(1994)
European Journal of Biochemistry
, vol.219
, Issue.1-2
, pp. 1-10
-
-
Liljas, A.1
Hakansson, K.2
Jonsson, B.H.3
Xue, Y.4
-
57
-
-
1642540579
-
Unexpected Nanomolar Inhibition of Carbonic Anhydrase by COX-2-Selective Celecoxib: New Pharmacological Opportunities Due to Related Binding Site Recognition
-
DOI 10.1021/jm030912m
-
Weber, A.; Casini, A.; Heine, A.; Kuhn, D.; Supuran, C. T.; Scozzafava, A.; Klebe, G. Unexpected nanomolar inhibition of carbonic anhydrase by COX-2-selective celecoxib: new pharmacological opportunities due to related binding site recognition J. Med. Chem. 2004, 47, 550-557 (Pubitemid 38129713)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.3
, pp. 550-557
-
-
Weber, A.1
Casini, A.2
Heine, A.3
Kuhn, D.4
Supuran, C.T.5
Scozzafava, A.6
Klebe, G.7
-
58
-
-
0032898499
-
Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease
-
Trylska, J.; Antosiewicz, J.; Geller, M.; Hodge, C. N.; Klabe, R. M.; Head, M. S.; Gilson, M. K. Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease Protein Sci. 1999, 8, 180-195 (Pubitemid 29035531)
-
(1999)
Protein Science
, vol.8
, Issue.1
, pp. 180-195
-
-
Trylska, J.1
Antosiewicz, J.2
Geller, M.3
Hodge, N.4
Klabe, R.M.5
Head, M.S.6
Gilson, M.K.7
-
59
-
-
34547657456
-
Atypical protonation states in the active site of HIV-1 protease: A computational study
-
DOI 10.1021/ci600522c
-
Czodrowski, P.; Sotriffer, C. A.; Klebe, G. Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study J. Chem. Inf. Model. 2007, 47, 1590-1598 (Pubitemid 47210062)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.4
, pp. 1590-1598
-
-
Czodrowski, P.1
Sotriffer, C.A.2
Klebe, G.3
-
60
-
-
0027181741
-
Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation
-
Harte, W. E.; Beveridge, D. L. Prediction of the protonation state of the active site aspartyl residues in HIV-1 protease-inhibitor complexes via molecular dynamics simulation J. Am. Chem. Soc. 1993, 115, 3883-3886 (Pubitemid 23236280)
-
(1993)
Journal of the American Chemical Society
, vol.115
, Issue.10
, pp. 3883-3886
-
-
Harte Jr., W.E.1
Beveridge, D.L.2
-
61
-
-
0028231388
-
Crystal structure of human protein tyrosine phosphatase 1B
-
Barford, D.; Flint, A. J.; Tonks, N. K. Crystal structure of human protein tyrosine phosphatase 1B Science 1994, 263, 1397-1404 (Pubitemid 24137822)
-
(1994)
Science
, vol.263
, Issue.5152
, pp. 1397-1404
-
-
Barford, D.1
Flint, A.J.2
Tonks, N.K.3
-
62
-
-
0034318309
-
Stabilization of Charges and Protonation States in the Active Site of the Protein Tyrosine Phosphatases: A Computational Study
-
Dillet, V.; Van Etten, R. L.; Bashford, D. Stabilization of Charges and Protonation States in the Active Site of the Protein Tyrosine Phosphatases: A Computational Study J. Phys. Chem. B 2000, 104, 11321-11333
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 11321-11333
-
-
Dillet, V.1
Van Etten, R.L.2
Bashford, D.3
-
63
-
-
65249151871
-
Prediction of SAMPL-1 Hydration Free Energies Using a Continuum Electrostatics-Dispersion Model
-
Sulea, T.; Wanapun, D.; Dennis, S.; Purisima, E. O. Prediction of SAMPL-1 Hydration Free Energies Using a Continuum Electrostatics-Dispersion Model J. Phys. Chem. B 2009, 113, 4511-4520
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4511-4520
-
-
Sulea, T.1
Wanapun, D.2
Dennis, S.3
Purisima, E.O.4
-
64
-
-
77953325045
-
Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge
-
Purisima, E.; Corbeil, C.; Sulea, T. Rapid prediction of solvation free energy. 3. Application to the SAMPL2 challenge J. Comput.-Aided Mol. Des. 2010, 24, 373-383
-
(2010)
J. Comput.-Aided Mol. Des.
, vol.24
, pp. 373-383
-
-
Purisima, E.1
Corbeil, C.2
Sulea, T.3
-
65
-
-
0038298792
-
Profiling charge complementarity and selectivity for binding at the protein surface
-
Sulea, T.; Purisima, E. O. Profiling charge complementarity and selectivity for binding at the protein surface Biophys. J. 2003, 84, 2883-2896 (Pubitemid 36531742)
-
(2003)
Biophysical Journal
, vol.84
, Issue.5
, pp. 2883-2896
-
-
Sulea, T.1
Purisima, E.O.2
|