-
1
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
DOI 10.1021/jm030489h
-
Ferrara, P., Gohlke, H., et al. (2004) Assessing Scoring Functions for Protein-Ligand Interactions, J. Med. Chem. 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., et al. (2004) An Extensive Test of 14 Scoring Functions Using the PDBbind Refined Set of 800 Protein-Ligand Complexes, J. Chem. Inf. Comput. Sci. 44 2114-2125.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
-
3
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G. L., Andrews, C.W., et al. (2006) A Critical Assessment of Docking Programs and Scoring Functions, J. Med. Chem. 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., and Klebe, G. (2002) Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors, Angew. Chem. Int. Ed. 41, 2644-2676.
-
(2002)
Angew. Chem. Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
5
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm, H. J. (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure, J. Comput.-Aided Mol. Des. 8, 243-256.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.J.1
-
6
-
-
0029995624
-
VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
-
DOI 10.1021/ja9539002
-
Head, R. D., Smythe, M. L., et al. (1996) VALIDATE: A New Method for the Receptor-Based Prediction of Binding Affinities of Novel Ligands, J. Amer. Chem. Soc. 118, 3959-3969. (Pubitemid 26168541)
-
(1996)
Journal of the American Chemical Society
, vol.118
, Issue.16
, pp. 3959-3969
-
-
Head, R.D.1
Smythe, M.L.2
Oprea, T.I.3
Waller, C.L.4
Green, S.M.5
Marshall, G.R.6
-
7
-
-
0031180937
-
Prediction of ligand-receptor binding thermodynamics by free energy force field (FEFF) 3D-QSAR analysis: Application to a set of peptidometic renin inhibitors
-
Tokarski, J. S., and Hopfinger, A. J. (1997) Prediction of Ligand-Receptor Binding Thermodynamics by Free Energy Force Field (FEFF) 3D-QSAR Analysis: Application to a Set of Peptidometic Renin Inhibitors, J. Chem. Inf. Comput. Sci. 37, 792-811. (Pubitemid 127603594)
-
(1997)
Journal of Chemical Information and Computer Sciences
, vol.37
, Issue.4
, pp. 792-811
-
-
Tokarski, J.S.1
Hopfinger, A.J.2
-
8
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M. D., Murray, C. W., et al. (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes, J. Comput.-Aided Mol. Des. 11, 425-445. (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
-
9
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
DOI 10.1023/A:1016357811882
-
Wang, R., Lai, L., and Wang, S. (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction, J. Comput.-Aided Mol. Des. 16, 11-26. (Pubitemid 34855041)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.1
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
10
-
-
0023659387
-
Semiquantitative calculations of catalytic free energies in genetically modified enzymes
-
Hwang, J. K., and Warshel, A. (1987) Semiquantitative Calculations of Catalytic Free Energies in Genetically Modified Enzymes, Biochemistry 26, 2669-2673.
-
(1987)
Biochemistry
, vol.26
, pp. 2669-2673
-
-
Hwang, J.K.1
Warshel, A.2
-
11
-
-
0035312864
-
Statistical potentials and scoring functions applied to protein-ligand binding
-
DOI 10.1016/S0959-440X(00)00195-0
-
Gohlke, H., and Klebe, G. (2001) Statistical potentials and scoring functions applied to protein-ligand binding, Curr. Opin. Struct. Biol. 11, 231-235. (Pubitemid 32289427)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.2
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
12
-
-
77955800755
-
Mean-force scoring functions for protein-ligand binding
-
Huang, S.-Y., and Zou, X. (2010) Mean-force scoring functions for protein-ligand binding, Annu. Rep. Comput. Chem. 6, 281-296.
-
(2010)
Annu. Rep. Comput. Chem.
, vol.6
, pp. 281-296
-
-
Huang, S.-Y.1
Zou, X.2
-
13
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
DOI 10.1021/jm980536j
-
Muegge, I., and Martin, Y. C. (1999) A General and Fast Scoring Function for Protein-Ligand Interactions: A Simplified Potential Approach, J. Med. Chem. 42, 791-804. (Pubitemid 29136170)
-
(1999)
Journal of Medicinal Chemistry
, vol.42
, Issue.5
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
14
-
-
77649221514
-
Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
-
Huang, S.-Y., and Zou, X. (2010) Inclusion of Solvation and Entropy in the Knowledge-Based Scoring Function for Protein-Ligand Interactions, J. Chem. Inf. Model. 50, 262-273.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 262-273
-
-
Huang, S.-Y.1
Zou, X.2
-
15
-
-
0037142298
-
SMall Molecule Growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
-
DOI 10.1021/jm0105833
-
Ishchenko, A. V., and Shakhnovich, E. I. (2002) SMall Molecule Growth 2001 (SMoG2001): An Improved Knowledge-Based Scoring Function for Protein-Ligand Interactions, J. Med. Chem. 45, 2770-2780. (Pubitemid 34627647)
-
(2002)
Journal of Medicinal Chemistry
, vol.45
, Issue.13
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich, E.I.2
-
16
-
-
33846863158
-
Solvated Interaction Energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space
-
DOI 10.1021/ci600406v
-
Naïm, M., Bhat, S., et al. (2007) Solvated interaction energy (SIE) for scoring proteinligand binding affinities. 1. Exploring the parameter space, J. Chem. Inf. Model. 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
-
17
-
-
44149094011
-
Molecular Dynamics -Solvated Interaction Energy Studies of Protein-Protein Interactions: The MP1-p14 Scaffolding Complex
-
Cui, Q., Sulea, T., et al. (2008) Molecular Dynamics -Solvated Interaction Energy Studies of Protein-Protein Interactions: the MP1-p14 Scaffolding Complex, J. Mol. Biol 379, 787-802.
-
(2008)
J. Mol. Biol
, vol.379
, pp. 787-802
-
-
Cui, Q.1
Sulea, T.2
-
18
-
-
0033536456
-
Inclusion of solvation in ligand binding free energy calculations using the generalized-born model
-
Zou, X., Sun, Y., and Kuntz, I. D. (1999) Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model, J. Amer. Chem. Soc. 121, 8033-8043.
-
(1999)
J. Amer. Chem. Soc.
, vol.121
, pp. 8033-8043
-
-
Zou, X.1
Sun, Y.2
Kuntz, I.D.3
-
19
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman, P. A., Massova, I., et al. (2000) Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models, Acc. Chem. Res. 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
-
20
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
Kuhn, B., Gerber, P., et al. (2005) Validation and Use of the MM-PBSA Approach for Drug Discovery, J. Med. Chem. 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
-
21
-
-
0347602124
-
Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
-
Gohlke, H., and Case, D. A. (2004) Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf, J. Comput. Chem. 25, 238-250.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
22
-
-
0036280661
-
Ligand binding affinities from MD simulations
-
Åqvist, J., Luzhkov, V. B., and Brandsdal, B. O. (2002) Ligand Binding Affinities from MD Simulations, Acc. Chem. Res. 35, 358-365.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 358-365
-
-
Åqvist, J.1
Luzhkov, V.B.2
Brandsdal, B.O.3
-
24
-
-
5644287368
-
Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm
-
Chang, C. E., and Gilson, M. K. (2004) Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm, J. Amer. Chem. Soc. 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
-
25
-
-
16344395749
-
Calculation of cyclodextrin binding affinities: Energy, entropy, and implications for drug design
-
DOI 10.1529/biophysj.104.049494
-
Chen, W., Chang, C. E., and Gilson, M. K. (2004) Calculation of Cyclodextrin Binding Affinities: Energy, Entropy, and Implications for Drug Design, Biophys. J. 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
-
26
-
-
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., and Bayly, C. I. (2002) Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: II. Parameterization and validation, J. Comput. Chem. 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
-
27
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C. I., Cieplak, P., et al. (1993) A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model, J. Phys. Chem. 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
-
28
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
Hornak, V., Abel, R., et al. (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters, Proteins Struct. Funct. Bioinf. 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
-
29
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J., Wolf, R. M., et al. (2004) Development and testing of a general amber force field, J. Comput. Chem. 25, 1157-1174.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
-
30
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., Wu, C., et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem. 24, 1999-2012.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
-
31
-
-
76249085850
-
How to obtain statistically converged MM/GBSA results
-
Genheden, S., and Ryde, U. (2010) How to obtain statistically converged MM/GBSA results, J. Comput. Chem. 31, 837-846.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 837-846
-
-
Genheden, S.1
Ryde, U.2
-
32
-
-
77952786003
-
Accurate ensemble molecular dynamics binding free energy ranking of multidrug-resistant HIV-1 proteases
-
Sadiq, S. K., Wright, D. W., et al. (2010) Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases, J. Chem. Inf. Model. 50, 890-905.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 890-905
-
-
Sadiq, S.K.1
Wright, D.W.2
-
33
-
-
70350501157
-
Predictions of binding for dopamine D2 receptor antagonists by the SIE method
-
Wang, Y. T., Su, Z. Y., et al. (2009) Predictions of Binding for Dopamine D2 Receptor Antagonists by the SIE Method, J. Chem. Inf. Model. 49, 2369-2375.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2369-2375
-
-
Wang, Y.T.1
Su, Z.Y.2
-
34
-
-
67349148279
-
Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. in silico and in vitro mutagenesis
-
Wimmerová, M., Mishra, N., et al. (2009) Importance of oligomerisation on Pseudomonas aeruginosa Lectin-II binding affinity. In silico and in vitro mutagenesis, J. Mol. Model. 15, 673-679.
-
(2009)
J. Mol. Model.
, vol.15
, pp. 673-679
-
-
Wimmerová, M.1
Mishra, N.2
-
35
-
-
77955769458
-
Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations
-
Mishra, N. K., Kríz, Z., et al. (2010) Recognition of selected monosaccharides by Pseudomonas aeruginosa Lectin II analyzed by molecular dynamics and free energy calculations, Carbohydr. Res. 345, 1432-1441.
-
(2010)
Carbohydr. Res.
, vol.345
, pp. 1432-1441
-
-
Mishra, N.K.1
Kríz, Z.2
-
36
-
-
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., and Wittung-Stafshede, P. (2008) Stability and ATP Binding of the Nucleotide-binding Domain of the Wilson Disease Protein: Effect of the Common H1069Q Mutation, J. Mol. Biol. 383, 1097-1111.
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 1097-1111
-
-
Rodriguez-Granillo, A.1
Sedlak, E.2
Wittung-Stafshede, P.3
-
37
-
-
77955557080
-
Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields
-
Wei, C., Mei, Y., and Zhang, D. (2010) Theoretical study on the HIV-1 integrase-5CITEP complex based on polarized force fields, Chem. Phys. Lett. 495, 121-124.
-
(2010)
Chem. Phys. Lett.
, vol.495
, pp. 121-124
-
-
Wei, C.1
Mei, Y.2
Zhang, D.3
-
38
-
-
33947718470
-
The S2 subsites of cathepsins K and L and their contribution to collagen degradation
-
DOI 10.1110/ps.062666607
-
Lecaille, F., Chowdhury, S., et al. (2007) The S2 subsites of cathepsins K and L and their contribution to collagen degradation, Protein Sci. 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
-
39
-
-
37649023004
-
Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis
-
Nguyen, M., Marcellus, R. C., et al. (2007) Small molecule obatoclax (GX15-070) antagonizes MCL-1 and overcomes MCL-1-mediated resistance to apoptosis, Proc. Nat. Acad. Sci. U.S.A. 104, 19512-19517.
-
(2007)
Proc. Nat. Acad. Sci. U.S.A.
, vol.104
, pp. 19512-19517
-
-
Nguyen, M.1
Marcellus, R.C.2
-
40
-
-
77950037970
-
Structure-activity relationship of novel DAPK inhibitors identified by structure-based virtual screening
-
Okamoto, M., Takayama, K., et al. (2010) Structure-activity relationship of novel DAPK inhibitors identified by structure-based virtual screening, Bioorg. Med. Chem. 18, 2728-2734.
-
(2010)
Bioorg. Med. Chem.
, vol.18
, pp. 2728-2734
-
-
Okamoto, M.1
Takayama, K.2
|