-
1
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu AA, Shelenkov AA, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
-
(2003)
Protein Sci
, vol.12
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.3
-
2
-
-
34250792960
-
IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models
-
Hartmann C, Antes I, Lengauer T. IRECS: a new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci 2007;16:1294-1307.
-
(2007)
Protein Sci
, vol.16
, pp. 1294-1307
-
-
Hartmann, C.1
Antes, I.2
Lengauer, T.3
-
3
-
-
0035838974
-
Extending the accuracy limits of prediction for side-chain conformations
-
Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001;311:421-430.
-
(2001)
J Mol Biol
, vol.311
, pp. 421-430
-
-
Xiang, Z.1
Honig, B.2
-
4
-
-
33749004010
-
How inaccuracies in protein structure models affect estimates of protein-ligand interactions: Computational analysis of HIV-I protease inhibitor binding
-
Thorsteinsdottir HB, Schwede T, Zoete V, Meuwly M. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Proteins 2006;65:407-423.
-
(2006)
Proteins
, vol.65
, pp. 407-423
-
-
Thorsteinsdottir, H.B.1
Schwede, T.2
Zoete, V.3
Meuwly, M.4
-
5
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
6
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claufien H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 2001;308:377-395.
-
(2001)
J Mol Biol
, vol.308
, pp. 377-395
-
-
Claufien, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
7
-
-
0033674405
-
Virtual screening with solvation and ligand induced complementarity
-
Schnecke V, Kuhn LA. Virtual screening with solvation and ligand induced complementarity. Perspect Drug Disc Des 2000;20:171-190.
-
(2000)
Perspect Drug Disc Des
, vol.20
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.A.2
-
8
-
-
0031965676
-
Flexible ligand docking using conformational ensembles
-
Lorber DM, Shoichet BK. Flexible ligand docking using conformational ensembles. Protein Sci 1998;7:938-950.
-
(1998)
Protein Sci
, vol.7
, pp. 938-950
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
9
-
-
0036108486
-
Protein-protein docking with multiple residue conformations and residue substitutions
-
Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci 2002;11:1393-1408.
-
(2002)
Protein Sci
, vol.11
, pp. 1393-1408
-
-
Lorber, D.M.1
Udo, M.K.2
Shoichet, B.K.3
-
10
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei BQ, Weaver LH, Ferrari AM, Matthews BW, Shoichet BK. Testing a flexible-receptor docking algorithm in a model binding site. J Mol Biol 2004;337:1161-1182.
-
(2004)
J Mol Biol
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
Weaver, L.H.2
Ferrari, A.M.3
Matthews, B.W.4
Shoichet, B.K.5
-
11
-
-
0347123444
-
Ligand-supported homology modeling of g-protein-coupled receptor sites: Models sufficient for successful virtual screening
-
Evers A, Klebe G. Ligand-supported homology modeling of g-protein-coupled receptor sites: models sufficient for successful virtual screening. Angew Chem Int Ed Eng 2004;43:248-251.
-
(2004)
Angew Chem Int Ed Eng
, vol.43
, pp. 248-251
-
-
Evers, A.1
Klebe, G.2
-
12
-
-
6044260116
-
Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model
-
Evers A, Klebe G. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model. J Med Chem 2004;47:5381-5392.
-
(2004)
J Med Chem
, vol.47
, pp. 5381-5392
-
-
Evers, A.1
Klebe, G.2
-
13
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 2006;49:534-553.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
14
-
-
0025341310
-
Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins
-
Sippl MJ. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. J Mol Biol 1990;213:859-883.
-
(1990)
J Mol Biol
, vol.213
, pp. 859-883
-
-
Sippl, M.J.1
-
15
-
-
0033954256
-
The Protein Data Bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 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
-
16
-
-
33745634395
-
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658-1659.
-
Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658-1659.
-
-
-
-
17
-
-
1842326139
-
Bayesian statistical analysis of protein side-chain rotamer preferences
-
Dunbrack RL, Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6:1661-1681.
-
(1997)
Protein Sci
, vol.6
, pp. 1661-1681
-
-
Dunbrack, R.L.1
Cohen, F.E.2
-
18
-
-
0032488962
-
An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
-
Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916.
-
(1998)
J Mol Biol
, vol.275
, pp. 895-916
-
-
Samudrala, R.1
Moult, J.2
-
19
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006;49:6789-6801.
-
(2006)
J Med Chem
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
21
-
-
0029565303
-
A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling
-
Koehl P, Delarue M. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat Struct Biol 1995;2:163-170.
-
(1995)
Nat Struct Biol
, vol.2
, pp. 163-170
-
-
Koehl, P.1
Delarue, M.2
-
22
-
-
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
-
23
-
-
15244346501
-
LigScore: A novel scoring function for predicting binding affinities
-
Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M. LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 2005;23:395-407.
-
(2005)
J Mol Graph Model
, vol.23
, pp. 395-407
-
-
Krammer, A.1
Kirchhoff, P.D.2
Jiang, X.3
Venkatachalam, C.M.4
Waldman, M.5
-
24
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, Fogel LJ, Freer ST. 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
Fogel, L.J.6
Freer, S.T.7
-
25
-
-
0001745748
-
Effect of ligand volume correction on PMF scoring
-
Muegge I. Effect of ligand volume correction on PMF scoring. J Comput Chem 2001;4:418-425.
-
(2001)
J Comput Chem
, vol.4
, pp. 418-425
-
-
Muegge, I.1
-
26
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge I, Martin YC. 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
-
27
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design ofenzyme inhibitors
-
Böhm HJ. The computer program LUDI: a new method for the de novo design ofenzyme inhibitors. J Comput Aided Mol Des 1992;6:61-78.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 61-78
-
-
Böhm, H.J.1
-
28
-
-
0027027467
-
LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
-
Böhm HJ. LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 1992;6:593-606.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 593-606
-
-
Böhm, H.J.1
-
29
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Bohm HJ. 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
-
-
Bohm, H.J.1
-
30
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones G, Willett P, Glen RC. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995;245:43-53.
-
(1995)
J Mol Biol
, vol.245
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
31
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
-
(1997)
J Mol Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
32
-
-
0035025191
-
DOCK 4.0: Searchstrategies for automated molecular docking of flexible molecule databases
-
Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: searchstrategies for automated molecular docking of flexible molecule databases. J Comput Aid Mol Des 2001;15:411-428.
-
(2001)
J Comput Aid Mol Des
, vol.15
, pp. 411-428
-
-
Ewing, T.J.A.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
33
-
-
0031226772
-
Empirical scoring functions. I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. 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
-
34
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
-
Morris GM, Goodsel DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J Comp Chem 1998;19:1639-1662.
-
(1998)
J Comp Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsel, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
35
-
-
0021757436
-
A new force field for molecular mechanical simulation ofnucleic acids and proteins
-
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S Jr, Weiner PK. A new force field for molecular mechanical simulation ofnucleic 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 Jr, S.7
Weiner, P.K.8
-
36
-
-
84988053694
-
An all atom force field for simulations of proteins and nucleic acids
-
Weiner SJ, Kollman PA, Nguyen DT, Case DA. An all atom force field for simulations of proteins and nucleic acids. J Comp Chem 1986;7:230-252.
-
(1986)
J Comp Chem
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, D.T.3
Case, D.A.4
-
37
-
-
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
-
38
-
-
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
-
39
-
-
33750555073
-
An iterative knowledge-based scoring function to predict protein-ligand interactions. I. Derivation of interaction potentials
-
Huang SY, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions. I. Derivation of interaction potentials. J Comput Chem 2006;27:1866-1875.
-
(2006)
J Comput Chem
, vol.27
, pp. 1866-1875
-
-
Huang, S.Y.1
Zou, X.2
-
40
-
-
33750574927
-
An iterative knowledge-based scoring function to predict protein-ligand interactions. II. Validation of the scoring function
-
Huang SY, 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
-
41
-
-
84986432941
-
Automated docking with grid based energy evaluation
-
Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid based energy evaluation. 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
-
42
-
-
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
-
43
-
-
26444588137
-
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
43
-
43.Velec HFG, Gohlke H, Klebe G. DrugScore(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
-
45
-
-
0035812694
-
Protein structure prediction and structural genomics
-
Baker D, Sali A. Protein structure prediction and structural genomics. Science 2001;294:93-96.
-
(2001)
Science
, vol.294
, pp. 93-96
-
-
Baker, D.1
Sali, A.2
-
46
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
Stahl M, Rarey M. Detailed analysis of scoring functions for virtual screening. J Med Chem 2001;44:1035-1042.
-
(2001)
J Med Chem
, vol.44
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
47
-
-
33746924045
-
Ensemble docking into flexible active sites. critical evaluation of FlexE against JNK-3 and beta-secretase
-
Polgar T, Keserü GM. Ensemble docking into flexible active sites. critical evaluation of FlexE against JNK-3 and beta-secretase. J Chem Inf Model 2006;46:1795-1805.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 1795-1805
-
-
Polgar, T.1
Keserü, G.M.2
-
48
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger E, Rodrigo J, Muller P, Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 2004;57:225-242.
-
(2004)
Proteins
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
49
-
-
24944433024
-
Fast structure based virtual ligand screening combining FRED, DOCK, and Surflex
-
Miteva MA, Lee WH, Montes MO, Villoutreix BO. Fast structure based virtual ligand screening combining FRED, DOCK, and Surflex. J Med Chem 2005;48:6012-6022.
-
(2005)
J Med Chem
, vol.48
, pp. 6012-6022
-
-
Miteva, M.A.1
Lee, W.H.2
Montes, M.O.3
Villoutreix, B.O.4
-
50
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren GL, Andrews CW, Capelli AM, Clarke B, LaLonde J, Lambert MH, Lindvall M, Nevins N, Semus SF, Senger S, Tedesco G, Wall ID, Woolven JM, Peishoff CE, Head MS. A critical assessment of docking programs and scoring functions. J Med Chem 2006;49:5912-5931
-
(2006)
J Med Chem
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
51
-
-
0030076041
-
Placement of medium-sized molecular fragments into active sites of proteins
-
Rarey M, Wefing S, Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des 1996;10:41-54.
-
(1996)
J Comput Aided Mol Des
, vol.10
, pp. 41-54
-
-
Rarey, M.1
Wefing, S.2
Lengauer, T.3
-
52
-
-
84976668743
-
Algorithm 457: Finding all cliques of an undirected graph
-
Bron C, Kerbosch J. Algorithm 457: finding all cliques of an undirected graph. CACM 1973;16:575-577.
-
(1973)
CACM
, vol.16
, pp. 575-577
-
-
Bron, C.1
Kerbosch, J.2
-
53
-
-
0242301182
-
Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials
-
Evers A, Gohlke H, Klebe G. Ligand-supported homology modelling of protein binding-sites using knowledge-based potentials. J Mol Biol 2003;334:327-345.
-
(2003)
J Mol Biol
, vol.334
, pp. 327-345
-
-
Evers, A.1
Gohlke, H.2
Klebe, G.3
-
54
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
-
(1993)
J Mol Biol
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
55
-
-
17744387920
-
All are not equal: A benchmark of different homology modeling programs
-
Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci 2005;14:1315-1327.
-
(2005)
Protein Sci
, vol.14
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
|