-
2
-
-
77949977626
-
The use of scoring functions in drug discovery applications
-
Böhm H.J., Stahl M. The use of scoring functions in drug discovery applications. Rev. Comput. Chem. 2002, 18:41-87.
-
(2002)
Rev. Comput. Chem.
, vol.18
, pp. 41-87
-
-
Böhm, H.J.1
Stahl, M.2
-
3
-
-
0034979318
-
Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
-
Wang W., Donini O., Reyes C.M., Kollman P.A. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 2001, 30:211-243.
-
(2001)
Annu. Rev. Biophys. Biomol. Struct.
, vol.30
, pp. 211-243
-
-
Wang, W.1
Donini, O.2
Reyes, C.M.3
Kollman, P.A.4
-
4
-
-
0036680148
-
Lead discovery using molecular docking
-
Shoichet B.K., McGovern S.L., Wei B., Irwin J.J. Lead discovery using molecular docking. Curr. Opin. Chem. Biol. 2002, 6:439-446.
-
(2002)
Curr. Opin. Chem. Biol.
, vol.6
, pp. 439-446
-
-
Shoichet, B.K.1
McGovern, S.L.2
Wei, B.3
Irwin, J.J.4
-
7
-
-
33749513370
-
Scoring functions for protein-ligand docking
-
Jain A.N. Scoring functions for protein-ligand docking. Curr. Protein Pept. Sci. 2006, 7:407-420.
-
(2006)
Curr. Protein Pept. Sci.
, vol.7
, pp. 407-420
-
-
Jain, A.N.1
-
8
-
-
13444292556
-
Scoring functions for protein-ligand interactions: A critical perspective
-
Schulz-Gasch T., Stahl M. Scoring functions for protein-ligand interactions: A critical perspective. Drug Discov. Today Technol. 2004, 1:231-239.
-
(2004)
Drug Discov. Today Technol.
, vol.1
, pp. 231-239
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
9
-
-
34249278087
-
Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
-
Rajamani R., Good A.C. Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development. Curr. Opin. Drug. Discov. Devel. 2007, 10:308-315.
-
(2007)
Curr. Opin. Drug. Discov. Devel.
, vol.10
, pp. 308-315
-
-
Rajamani, R.1
Good, A.C.2
-
10
-
-
0035312864
-
Statistical potentials and scoring functions applied to protein-ligand binding
-
Gohlke H., Klebe G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol. 2001, 11:231-235.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
12
-
-
84986432941
-
Automated docking with grid-based energy approach to macromolecule-ligand interactions
-
Meng E.C., Shoichet B.K., Kuntz I.D. Automated docking with grid-based energy approach to macromolecule-ligand interactions. J. Comput. Chem. 1992, 13:505-524.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 505-524
-
-
Meng, E.C.1
Shoichet, B.K.2
Kuntz, I.D.3
-
13
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell D.S., Olson A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 1990, 8:195-202.
-
(1990)
Proteins
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
14
-
-
0033536456
-
Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model
-
Zou X., Sun Y., Kuntz I.D. Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model. J. Am. Chem. Soc. 1999, 121:8033-8043.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 8033-8043
-
-
Zou, X.1
Sun, Y.2
Kuntz, I.D.3
-
15
-
-
0036382728
-
A model binding site for testing scoring functions in molecular docking
-
Wei B.Q., Baase W.A., Weaver L.H., Matthews B.W., Shoichet B.K. A model binding site for testing scoring functions in molecular docking. J. Mol. Biol. 2002, 322:339-355.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 339-355
-
-
Wei, B.Q.1
Baase, W.A.2
Weaver, L.H.3
Matthews, B.W.4
Shoichet, B.K.5
-
16
-
-
2442562756
-
Pairwise GB/SA scoring function for structure-based drug design
-
Liu H.-Y., Kuntz I.D., Zou X. Pairwise GB/SA scoring function for structure-based drug design. J. Phys. Chem. B 2004, 108:5453-5462.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 5453-5462
-
-
Liu, H.-Y.1
Kuntz, I.D.2
Zou, X.3
-
17
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
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.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
18
-
-
33744821352
-
Electrostatics of ligand binding: Parametrization of the generalized born model and comparison with the Poisson-Boltzmann approach
-
Liu H.-Y., Zou X. Electrostatics of ligand binding: Parametrization of the generalized born model and comparison with the Poisson-Boltzmann approach. J. Phys. Chem. B 2006, 110:9304-9313.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 9304-9313
-
-
Liu, H.-Y.1
Zou, X.2
-
19
-
-
69549096119
-
Multiscale generalized Born modeling of ligand binding energies for virtual database screening
-
Liu H.-Y., Grinter S.Z., Zou X. Multiscale generalized Born modeling of ligand binding energies for virtual database screening. J. Phys. Chem. B 2009, 113:11793-11799.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 11793-11799
-
-
Liu, H.-Y.1
Grinter, S.Z.2
Zou, X.3
-
20
-
-
33746872935
-
Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
-
Lyne P.D., Lamb M.L., Saeh J.C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J. Med. Chem. 2006, 49:4805-4808.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 4805-4808
-
-
Lyne, P.D.1
Lamb, M.L.2
Saeh, J.C.3
-
21
-
-
45749138489
-
MM-GB/SA rescoring of docking poses in structure-based lead optimization
-
Guimaraes C.R.W., Cardozo M. MM-GB/SA rescoring of docking poses in structure-based lead optimization. J. Chem. Inf. Model. 2008, 48:958-970.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 958-970
-
-
Guimaraes, C.R.W.1
Cardozo, M.2
-
23
-
-
84986518863
-
AMBER-assisted model building with energy refinement¡ a general program for modeling molecules and their interactions
-
Weiner P.K., Kollman P.A. AMBER-assisted model building with energy refinement¡ a general program for modeling molecules and their interactions. J. Comput. Chem. 1981, 2:287-303.
-
(1981)
J. Comput. Chem.
, vol.2
, pp. 287-303
-
-
Weiner, P.K.1
Kollman, P.A.2
-
24
-
-
0021757436
-
A new force-field for molecular mechanical simulation of nucleic-acids and proteins
-
Weiner S.J., Kollman P.A., Case D.A., Singh U.C., Ghio C., Alagona G., Profeta S., Weiner P. A new force-field for molecular mechanical simulation of nucleic-acids and proteins. J. Am. Chem. Soc. 1984, 106:765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
25
-
-
84988053694
-
An all-atom force field for simulations of protein and nucleic acids
-
Weiner S.J., Kollman P.A., Nguyen D.T., Case D.A. An all-atom force field for simulations of protein and nucleic acids. J. Comput. Chem. 1986, 7:230-252.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
26
-
-
84988103838
-
Empirical energy functions for energy minimization and dynamics of nucleic acids
-
Nilsson L., Karplus M. Empirical energy functions for energy minimization and dynamics of nucleic acids. J. Comput. Chem. 1986, 7:591-616.
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 591-616
-
-
Nilsson, L.1
Karplus, M.2
-
27
-
-
84986512474
-
CHARMM a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
28
-
-
0030255303
-
Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
-
Jain A.N. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comput. Aided Mol. Des. 1996, 10:427-440.
-
(1996)
J. Comput. Aided Mol. Des.
, vol.10
, pp. 427-440
-
-
Jain, A.N.1
-
29
-
-
0029995624
-
Validate a new method for the receptor-based prediction of binding affinities of novel ligands
-
Head R.D., Smythe M.L., Oprea T.I., Waller C.L., Green S.M., Marshall G.R. Validate a new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 1996, 118:3959-3969.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, 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
-
30
-
-
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., Auton T.R., Paolini G.V., Mee R.P. 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. 1997, 11:425-445.
-
(1997)
J. Comput. Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
31
-
-
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. 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. 1994, 8:243-256.
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.J.1
-
32
-
-
0001704085
-
SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex
-
Wang R., Liu L., Lai L., Tang Y. SCORE: A new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Model. 1998, 4:379-394.
-
(1998)
J. Mol. Model.
, vol.4
, pp. 379-394
-
-
Wang, R.1
Liu, L.2
Lai, L.3
Tang, Y.4
-
33
-
-
0032112137
-
Prediction of binding constants of ptotein ligands: A fast method for the polarization of hits obtained from de novo design or 3D database search programs
-
Böhm H.J. Prediction of binding constants of ptotein ligands: A fast method for the polarization of hits obtained from de novo design or 3D database search programs. J. Comput. Aided Mol. Des. 1998, 12:309-323.
-
(1998)
J. Comput. Aided Mol. Des.
, vol.12
, pp. 309-323
-
-
Böhm, H.J.1
-
34
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar D.K., Verkhivker G.M., Rejto P.A., Sherman C.J., Fogel D.B., Freer S.T. Molecular recognition of the inhibitor AG-1343 by HIV-1 Protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 1995, 2:317-324.
-
(1995)
Chem. Biol.
, vol.2
, pp. 317-324
-
-
Gehlhaar, D.K.1
Verkhivker, G.M.2
Rejto, P.A.3
Sherman, C.J.4
Fogel, D.B.5
Freer, S.T.6
-
35
-
-
0039012103
-
-
American Chemical Society, Washington, DC, L. Parrill, M.R. Reddy (Eds.)
-
Gehlhaar D.K., Bouzida D., Rejto P.A. Rational Drug Design: Novel Methodology and Practical Applications 1999, 292-311. American Chemical Society, Washington, DC. L. Parrill, M.R. Reddy (Eds.).
-
(1999)
Rational Drug Design: Novel Methodology and Practical Applications
, pp. 292-311
-
-
Gehlhaar, D.K.1
Bouzida, D.2
Rejto, P.A.3
-
36
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R., Lai L., Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided Mol. Des. 2002, 16:11-26.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
37
-
-
0017021957
-
Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
-
Tanaka S., Scheraga H.A. Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules 1976, 9:945-950.
-
(1976)
Macromolecules
, vol.9
, pp. 945-950
-
-
Tanaka, S.1
Scheraga, H.A.2
-
38
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
-
Miyazawa S., Jernigan R.L. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 1985, 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
39
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force
-
Sippl M.J. Calculation of conformational ensembles from potentials of mean force. J. Mol. Biol. 1990, 213:859-883.
-
(1990)
J. Mol. Biol.
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
40
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
42
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich M., Lackner P., Weitckus S., Floeckner H., Froschauer R., Gottsbacher K., Casari G., Sippl M.J. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 1990, 216:167-180.
-
(1990)
J. Mol. Biol.
, vol.216
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
43
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones D.T., Taylor W.R., Thornton J.M. A new approach to protein fold recognition. Nature 1992, 358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
44
-
-
0029909384
-
An iterative method for extracting energy-like quantities from protein structures
-
Thomas P.D., Dill K.A. An iterative method for extracting energy-like quantities from protein structures. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:11628-11633.
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 11628-11633
-
-
Thomas, P.D.1
Dill, K.A.2
-
45
-
-
0029976427
-
Statistical potentials extracted from protein structures: How accurate are they?
-
Thomas P.D., Dill K.A. Statistical potentials extracted from protein structures: How accurate are they?. J. Mol. Biol. 1996, 257:457-469.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 457-469
-
-
Thomas, P.D.1
Dill, K.A.2
-
46
-
-
34247140654
-
-
Springer, New York, Y. Xu, D. Xu, J. Liang (Eds.)
-
Li X., Liang J. Computational Methods for Protein Structure Prediction and Modeling 2006, Vol. 1:71-124. Springer, New York. Y. Xu, D. Xu, J. Liang (Eds.).
-
(2006)
Computational Methods for Protein Structure Prediction and Modeling
, vol.1
, pp. 71-124
-
-
Li, X.1
Liang, J.2
-
47
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge I., Martin Y.C. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J. Med. Chem. 1999, 42:791-804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
48
-
-
77649221514
-
Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
-
Huang S.-Y., Zou X. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. J. Chem. Inf. Model. 2010, 50:262-273.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 262-273
-
-
Huang, S.-Y.1
Zou, X.2
-
49
-
-
33750555073
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials
-
Huang S.-Y., Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J. Comput. Chem. 2006, 27:1865-1875.
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1865-1875
-
-
Huang, S.-Y.1
Zou, X.2
-
50
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function
-
Huang S.-Y., Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J. Comput. Chem. 2006, 27:1876-1882.
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1876-1882
-
-
Huang, S.-Y.1
Zou, X.2
-
51
-
-
26444588137
-
CSD -knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
CSD -knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J. Med. Chem. 2005, 48:6296-6303.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
52
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke H., Hendlich M., Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 2000, 295:337-356.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
53
-
-
0037142298
-
Molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions
-
Ishchenko A.V., Shakhnovich Small E.I. molecule growth 2001 (SMoG2001): An improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem. 2002, 45:2770-2780.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich Small, E.I.2
-
54
-
-
0000823044
-
BLEEP-Potential of mean force describing protein-ligand interactions: I. Generating potential
-
Mitchell J.B.O., Laskowski R.A., Alex A., Thornton J.M. BLEEP-Potential of mean force describing protein-ligand interactions: I. Generating potential. J. Comput. Chem. 1999, 20:1165-1176.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1165-1176
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Thornton, J.M.4
-
55
-
-
0000882405
-
BLEEP-Potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data
-
Mitchell J.B.O., Laskowski R.A., Alex A., Forster M.J., Thornton J.M. BLEEP-Potential of mean force describing protein-ligand interactions: II. Calculation of binding energies and comparison with experimental data. J. Comput. Chem. 1999, 20:1177-1185.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1177-1185
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alex, A.3
Forster, M.J.4
Thornton, J.M.5
-
56
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang C., Liu S., Zhu Q., Zhou Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 2005, 48:2325-2335.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
57
-
-
49449086540
-
An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA
-
Zhao X., Liu X., Wang Y., Chen Z., Kang L., Zhang H., Luo X., Zhu W., Chen K., Li H., Wang X., Jiang H. An improved PMF scoring function for universally predicting the interactions of a ligand with protein, DNA, and RNA. J. Chem. Inf. Model. 2008, 48:1438-1447.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1438-1447
-
-
Zhao, X.1
Liu, X.2
Wang, Y.3
Chen, Z.4
Kang, L.5
Zhang, H.6
Luo, X.7
Zhu, W.8
Chen, K.9
Li, H.10
Wang, X.11
Jiang, H.12
-
58
-
-
0028881193
-
Empirical free eenrgy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
-
Verkhivker G., Appelt K., Freer S.T., Villafranca J.E. Empirical free eenrgy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8:677-691.
-
(1995)
Protein Eng.
, vol.8
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
59
-
-
0000934205
-
SMoG: de Novo design method based on simple, fast, and accutate free energy estimate. 1. Methodology and supporting evidence
-
DeWitte R.S., Shakhnovich E.I. SMoG: de Novo design method based on simple, fast, and accutate free energy estimate. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 1996, 118:11733-11744.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11733-11744
-
-
DeWitte, R.S.1
Shakhnovich, E.I.2
-
60
-
-
0035339739
-
Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes
-
Nobeli I., Mitchell J.B.O., Alex A., Thornton J.M. Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes. J. Comput. Chem. 2001, 22:673-688.
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 673-688
-
-
Nobeli, I.1
Mitchell, J.B.O.2
Alex, A.3
Thornton, J.M.4
-
61
-
-
0037046545
-
Docking into knowledge-based potential fields: A comparative evaluation of DrugScore
-
Sotriffer C.A., Gohlke H., Klebe G. Docking into knowledge-based potential fields: A comparative evaluation of DrugScore. J. Med. Chem. 2002, 45:1967-1970.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 1967-1970
-
-
Sotriffer, C.A.1
Gohlke, H.2
Klebe, G.3
-
62
-
-
0001752768
-
The Cambridge Structural Database: A quarter of a million crystal structures and rising
-
Allen F.H. The Cambridge Structural Database: A quarter of a million crystal structures and rising. Acta Crystallogr. 2002, B58:380-388.
-
(2002)
Acta Crystallogr.
, vol.58 B
, pp. 380-388
-
-
Allen, F.H.1
-
63
-
-
33749239216
-
M-Score: A new knowledge-based potential scoring function accounting for protein atom mobility
-
Yang C.-Y., Wang R., Wang S. M-Score: A new knowledge-based potential scoring function accounting for protein atom mobility. J. Med. Chem. 2006, 49:5903-5911.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5903-5911
-
-
Yang, C.-Y.1
Wang, R.2
Wang, S.3
-
64
-
-
26444468103
-
General and targeted statistical potentials for protein-ligand interactions
-
Mooij W.T., Verdonk M.L. General and targeted statistical potentials for protein-ligand interactions. Proteins 2005, 61:272-287.
-
(2005)
Proteins
, vol.61
, pp. 272-287
-
-
Mooij, W.T.1
Verdonk, M.L.2
-
65
-
-
0033566211
-
Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
-
Muegge I., Martin Y.C., Hajduk P.J., Fesik S.W. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J. Med. Chem. 1999, 42:2498-2503.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2498-2503
-
-
Muegge, I.1
Martin, Y.C.2
Hajduk, P.J.3
Fesik, S.W.4
-
66
-
-
0034081944
-
Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors
-
Ha S., Andreani R., Robbins A., Muegge I. Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors. J. Comput. Aided Mol. Des. 2000, 14:435-448.
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, pp. 435-448
-
-
Ha, S.1
Andreani, R.2
Robbins, A.3
Muegge, I.4
-
67
-
-
33749242403
-
PMF scoring revisited
-
Muegge I. PMF scoring revisited. J. Med. Chem. 2006, 49:5895-5902.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5895-5902
-
-
Muegge, I.1
-
68
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou H., Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 2002, 11:2714-2726.
-
(2002)
Protein Sci.
, vol.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
69
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang R., Lu Y., Wang S. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46:2287-2303.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
70
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
Huang S.-Y., Zou X. Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking. Proteins 2007, 66:399-421.
-
(2007)
Proteins
, vol.66
, pp. 399-421
-
-
Huang, S.-Y.1
Zou, X.2
-
71
-
-
33845923184
-
Efficient molecular docking of NMR structures: Application to HIV-1 protease
-
Huang S.-Y., Zou X. Efficient molecular docking of NMR structures: Application to HIV-1 protease. Protein Sci. 2007, 16:43-51.
-
(2007)
Protein Sci.
, vol.16
, pp. 43-51
-
-
Huang, S.-Y.1
Zou, X.2
-
72
-
-
46449084711
-
An iterative knowledge-based scoring function for protein-protein recognition
-
Huang S.-Y., Zou X. An iterative knowledge-based scoring function for protein-protein recognition. Proteins 2008, 72:557-579.
-
(2008)
Proteins
, vol.72
, pp. 557-579
-
-
Huang, S.-Y.1
Zou, X.2
-
73
-
-
0346996357
-
Improving structure-based virtual screening by multivariate analysis of scoring data
-
Jasobsson M., Lidén P., Stjernschantz E., Boström H., Norinder U. Improving structure-based virtual screening by multivariate analysis of scoring data. J. Med. Chem. 2003, 46:5781-5789.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 5781-5789
-
-
Jasobsson, M.1
Lidén, P.2
Stjernschantz, E.3
Boström, H.4
Norinder, U.5
|