-
2
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
-
(2002)
Proteins
, vol.47
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
4
-
-
0036007208
-
Virtual screening and fast automated docking methods
-
Schneider G, Bohm HJ. Virtual screening and fast automated docking methods. Drug Discov Today 2002;7:64-70.
-
(2002)
Drug Discov Today
, vol.7
, pp. 64-70
-
-
Schneider, G.1
Bohm, H.J.2
-
5
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL 3rd. Assessing scoring functions for protein-ligand interactions. J Med Chem 2004;47:3032-3047.
-
(2004)
J Med Chem
, vol.47
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Brooks III, C.L.5
-
6
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 2001;15:411-428.
-
(2001)
J Comput Aided Mol Des
, vol.15
, pp. 411-428
-
-
Ewing, T.J.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
7
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell DS, Morris GM, Olson AJ. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 1996;9:1-5.
-
(1996)
J Mol Recognit
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
8
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 2002;46:34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
9
-
-
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
-
10
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Willett P, Glen RC, Leach AR, Taylor R, Jones G. 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
-
-
Willett, P.1
Glen, R.C.2
Leach, A.R.3
Taylor, R.4
Jones, G.5
-
11
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola E, Walters WP, Charifson PS. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004;56:235-249.
-
(2004)
Proteins
, vol.56
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
12
-
-
0036022957
-
Modified AutoDock for accurate docking of protein kinase inhibitors
-
Buzko OV, Bishop AC, Shokat KM. Modified AutoDock for accurate docking of protein kinase inhibitors. J Comput Aided Mol Des 2002;16:113-127.
-
(2002)
J Comput Aided Mol Des
, vol.16
, pp. 113-127
-
-
Buzko, O.V.1
Bishop, A.C.2
Shokat, K.M.3
-
13
-
-
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
-
14
-
-
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
-
15
-
-
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
-
16
-
-
0032153192
-
Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model
-
Murray CW, Auton TR, Eldridge MD. Empirical scoring functions. II. The testing of an empirical scoring function for the prediction of ligand-receptor binding affinities and the use of Bayesian regression to improve the quality of the model. J Comput Aided Mol Des 1998;12:503-519.
-
(1998)
J Comput Aided Mol Des
, vol.12
, pp. 503-519
-
-
Murray, C.W.1
Auton, T.R.2
Eldridge, M.D.3
-
17
-
-
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
-
18
-
-
15244353539
-
Side-chain flexibility in protein-ligand binding: The minimal rotation hypothesis
-
Zavodszky MI, Kuhn LA. Side-chain flexibility in protein-ligand binding: the minimal rotation hypothesis. Protein Sci 2005;14:1104-1114.
-
(2005)
Protein Sci
, vol.14
, pp. 1104-1114
-
-
Zavodszky, M.I.1
Kuhn, L.A.2
-
19
-
-
0031302358
-
Flexible protein-ligand docking by global energy optimization in internal coordinates
-
Totrov M, Abagyan R. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 1997; Suppl 1:215-220.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 215-220
-
-
Totrov, M.1
Abagyan, R.2
-
20
-
-
0001238611
-
Protein-ligand docking as an energy optimization problem
-
Totrov M, Abagyan R. Protein-ligand docking as an energy optimization problem. Drug Receptor Thermodynamics 2001:603-624.
-
(2001)
Drug Receptor Thermodynamics
, pp. 603-624
-
-
Totrov, M.1
Abagyan, R.2
-
21
-
-
0035416126
-
High-throughput docking for lead generation
-
Abagyan R, Totrov M. High-throughput docking for lead generation. Curr Opin Chem Biol 2001;5:375-382.
-
(2001)
Curr Opin Chem Biol
, vol.5
, pp. 375-382
-
-
Abagyan, R.1
Totrov, M.2
-
22
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto CN, Abagyan RA. Protein flexibility in ligand docking and virtual screening to protein kinases. J Mol Biol 2004;337:209-225.
-
(2004)
J Mol Biol
, vol.337
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
23
-
-
0042282803
-
FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
-
Taylor RD, Jewsbury PJ, Essex JW. FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function. J Comput Chem 2003;24:1637-1656.
-
(2003)
J Comput Chem
, vol.24
, pp. 1637-1656
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
24
-
-
27144484954
-
Receptor flexibility in de novo ligand design and docking
-
Alberts IL, Todorov NP, Dean PM. Receptor flexibility in de novo ligand design and docking. J Med Chem 2005;48:6585-6596.
-
(2005)
J Med Chem
, vol.48
, pp. 6585-6596
-
-
Alberts, I.L.1
Todorov, N.P.2
Dean, P.M.3
-
25
-
-
25144445530
-
-
Schroedinger. New York: Schroedinger
-
Schroedinger. Glide 2.5. New York: Schroedinger; 2003.
-
(2003)
Glide 2.5
-
-
-
26
-
-
0031181346
-
QXP: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C, Bohacek RS. QXP: powerful, rapid computer algorithms for structure-based drug design. J Comput Aided Mol Des 1997;11:333-344.
-
(1997)
J Comput Aided Mol Des
, vol.11
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
27
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen 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
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
28
-
-
0038161052
-
Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
-
Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
-
(2003)
J Mol Biol
, vol.331
, pp. 281-299
-
-
Gray, J.J.1
Moughon, S.2
Wang, C.3
Schueler-Furman, O.4
Kuhlman, B.5
Rohl, C.A.6
Baker, D.7
-
29
-
-
17744364070
-
Improved side-chain modeling for protein-protein docking
-
Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
-
(2005)
Protein Sci
, vol.14
, pp. 1328-1339
-
-
Wang, C.1
Schueler-Furman, O.2
Baker, D.3
-
30
-
-
0038697805
-
Protein-protein docking predictions for the CAPRI experiment
-
Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins 2003;52:118-122.
-
(2003)
Proteins
, vol.52
, pp. 118-122
-
-
Gray, J.J.1
Moughon, S.E.2
Kortemme, T.3
Schueler-Furman, O.4
Misura, K.M.5
Morozov, A.V.6
Baker, D.7
-
31
-
-
21644459373
-
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
-
Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
-
(2005)
Proteins
, vol.60
, pp. 187-194
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
32
-
-
0036300662
-
Accurate computer-based design of a new backbone conformation in the second turn of protein L
-
Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D. Accurate computer-based design of a new backbone conformation in the second turn of protein L. J Mol Biol 2002;315:471-477.
-
(2002)
J Mol Biol
, vol.315
, pp. 471-477
-
-
Kuhlman, B.1
O'Neill, J.W.2
Kim, D.E.3
Zhang, K.Y.4
Baker, D.5
-
33
-
-
0345306764
-
Design of a novel globular protein fold with atomic level accuracy
-
Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic level accuracy. Science 2003;302:1364-1368.
-
(2003)
Science
, vol.302
, pp. 1364-1368
-
-
Kuhlman, B.1
Dantas, G.2
Ireton, G.C.3
Varani, G.4
Stoddard, B.L.5
Baker, D.6
-
34
-
-
1042298843
-
Computational design of protein-protein interactions
-
Kortemme T, Baker D. Computational design of protein-protein interactions. Curr Opin Chem Biol 2004;8:91-97.
-
(2004)
Curr Opin Chem Biol
, vol.8
, pp. 91-97
-
-
Kortemme, T.1
Baker, D.2
-
35
-
-
1842577654
-
Computational redesign of protein-protein interaction specificity
-
Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, Baker D. Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 2004;11:371-379.
-
(2004)
Nat Struct Mol Biol
, vol.11
, pp. 371-379
-
-
Kortemme, T.1
Joachimiak, L.A.2
Bullock, A.N.3
Schuler, A.D.4
Stoddard, B.L.5
Baker, D.6
-
36
-
-
0035950051
-
Ligand-protein database: Linking protein-ligand complex structures to binding data
-
Roche O, Kiyama R, Brooks CL 3rd. Ligand-protein database: linking protein-ligand complex structures to binding data. J Med Chem 2001;44:3592-3598.
-
(2001)
J Med Chem
, vol.44
, pp. 3592-3598
-
-
Roche, O.1
Kiyama, R.2
Brooks III, C.L.3
-
37
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
38
-
-
0027160197
-
Backbone-dependent rotamer library for proteins. Application to side-chain prediction
-
Dunbrack RL Jr, Karplus M. Backbone-dependent rotamer library for proteins. Application to side-chain prediction. J Mol Biol 1993;230:543-574.
-
(1993)
J Mol Biol
, vol.230
, pp. 543-574
-
-
Dunbrack Jr., R.L.1
Karplus, M.2
-
39
-
-
0031576989
-
Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: A new homology modeling tool
-
Bower MJ, Cohen FE, Dunbrack RL Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
-
(1997)
J Mol Biol
, vol.267
, pp. 1268-1282
-
-
Bower, M.J.1
Cohen, F.E.2
Dunbrack Jr., R.L.3
-
40
-
-
0037470581
-
An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
-
Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
-
(2003)
J Mol Biol
, vol.326
, pp. 1239-1259
-
-
Kortemme, T.1
Morozov, A.V.2
Baker, D.3
-
41
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4:187-217.
-
(1983)
J Comp 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
-
42
-
-
0000224283
-
CHARMM: The energy function and its parameterization with an overview of the program
-
Chichester: Wiley
-
MacKerell AD Jr, Brooks BR, Brooks CL, Nilsson L, Roux B, Won Y, Karplus M. CHARMM: The energy function and its parameterization with an overview of the program. In: The Encyclopedia of Computational Chemistry. Vol. 1. Chichester: Wiley; 1998. p 271-277.
-
(1998)
The Encyclopedia of Computational Chemistry
, vol.1
, pp. 271-277
-
-
MacKerell Jr., A.D.1
Brooks, B.R.2
Brooks, C.L.3
Nilsson, L.4
Roux, B.5
Won, Y.6
Karplus, M.7
-
43
-
-
0242593434
-
Development and current status of the CHARMM force field for nucleic acids
-
MacKerell AD Jr, Banavali N, Foloppe N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers 2000;56:257-265.
-
(2000)
Biopolymers
, vol.56
, pp. 257-265
-
-
MacKerell Jr., A.D.1
Banavali, N.2
Foloppe, N.3
-
44
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999;34:82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
45
-
-
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
-
46
-
-
0017411710
-
The Protein Data Bank: A computer-based archival file for macromolecular structures
-
Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr., Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
-
(1977)
J Mol Biol
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer Jr., E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
47
-
-
0036616218
-
The Protein Data Bank
-
Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002;58:899-907.
-
(2002)
Acta Crystallogr D Biol Crystallogr
, vol.58
, pp. 899-907
-
-
Berman, H.M.1
Battistuz, T.2
Bhat, T.N.3
Bluhm, W.F.4
Bourne, P.E.5
Burkhardt, K.6
Feng, Z.7
Gilliland, G.L.8
Iype, L.9
Jain, S.10
Fagan, P.11
Marvin, J.12
Padilla, D.13
Ravichandran, V.14
Schneider, B.15
Thanki, N.16
Weissig, H.17
Westbrook, J.D.18
Zardecki, C.19
-
48
-
-
0032738842
-
Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking
-
Kramer B, Rarey M, Lengauer T. Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking. Proteins 1999;37:228-241.
-
(1999)
Proteins
, vol.37
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
49
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
McGovern SL, Shoichet BK. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J Med Chem 2003;46:2895-2907.
-
(2003)
J Med Chem
, vol.46
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
50
-
-
2442640122
-
Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness
-
Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci 2004;13:1660-1669.
-
(2004)
Protein Sci
, vol.13
, pp. 1660-1669
-
-
Schlosshauer, M.1
Baker, D.2
-
51
-
-
2442449534
-
Modeling structurally variable regions in homologous proteins with rosetta
-
Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
-
(2004)
Proteins
, vol.55
, pp. 656-677
-
-
Rohl, C.A.1
Strauss, C.E.2
Chivian, D.3
Baker, D.4
-
52
-
-
0034641749
-
Native protein sequences are close to optimal for their structures
-
Kuhlman B, Baker D. Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci U S A 2000;97:10383-10388.
-
(2000)
Proc Natl Acad Sci U S A
, vol.97
, pp. 10383-10388
-
-
Kuhlman, B.1
Baker, D.2
|