-
2
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161:269-288.
-
(1982)
J Mol Biol
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
3
-
-
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
-
5
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar DK, Verkhivker GM, Rejio 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
Rejio, P.A.3
Sherman, C.J.4
Fogel, D.B.5
Fogel, L.J.6
Freer, S.T.7
-
6
-
-
0030154893
-
Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
-
Welch W, Ruppert J, Jain AN. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 1996;3:449-462.
-
(1996)
Chem Biol
, vol.3
, pp. 449-462
-
-
Welch, W.1
Ruppert, J.2
Jain, A.N.3
-
7
-
-
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
-
8
-
-
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
-
9
-
-
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;1:215-220.
-
(1997)
Proteins
, vol.1
, pp. 215-220
-
-
Totrov, M.1
Abagyan, R.2
-
10
-
-
0032533791
-
Flexible docking using Tabu search and an empirical estimate of binding affinity
-
Baxter CA, Murray CW, Clark DE, Westhead DR, Eldridge MD. Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins 1998;33:367-382.
-
(1998)
Proteins
, vol.33
, pp. 367-382
-
-
Baxter, C.A.1
Murray, C.W.2
Clark, D.E.3
Westhead, D.R.4
Eldridge, M.D.5
-
11
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G, Goodsell D, Halliday R, Huey R, Hart W, Belew R, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
-
(1998)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.1
Goodsell, D.2
Halliday, R.3
Huey, R.4
Hart, W.5
Belew, R.6
Olson, A.J.7
-
12
-
-
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
-
13
-
-
0035144771
-
Ligand-receptor docking with the Mining Minima optimizer
-
David L, Luo R, Gilson MK. Ligand-receptor docking with the Mining Minima optimizer. J Comput Aided Mol Des 2001;15:157-171.
-
(2001)
J Comput Aided Mol Des
, vol.15
, pp. 157-171
-
-
David, L.1
Luo, R.2
Gilson, M.K.3
-
14
-
-
0035342434
-
High throughput docking for library design and library prioritization
-
Diller DJ, Merz KM Jr. High throughput docking for library design and library prioritization. Proteins 2001;43:113-124.
-
(2001)
Proteins
, vol.43
, pp. 113-124
-
-
Diller, D.J.1
Merz Jr., K.M.2
-
15
-
-
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
-
16
-
-
0035976367
-
EUDOC a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
-
Pang YP, Perola E, Xu K, Prendergast FG. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J Comput Chem 2001;22:1750-1771.
-
(2001)
J Comput Chem
, vol.22
, pp. 1750-1771
-
-
Pang, Y.P.1
Perola, E.2
Xu, K.3
Prendergast, F.G.4
-
17
-
-
0036022961
-
Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
-
Jackson RM. Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space. J Comput Aided Mol Des 2002;16:43-57.
-
(2002)
J Comput Aided Mol Des
, vol.16
, pp. 43-57
-
-
Jackson, R.M.1
-
18
-
-
0036606204
-
ConsDock: A new program for the consensus analysis of protein-ligand interactions
-
Paul N, Rognan D. ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins 2002;47:521-533.
-
(2002)
Proteins
, vol.47
, pp. 521-533
-
-
Paul, N.1
Rognan, D.2
-
19
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
-
Zavodszky MI, Sanschagrin PC, Korde RS, Kuhn LA. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des 2002;16:883-902.
-
(2002)
J Comput Aided Mol Des
, vol.16
, pp. 883-902
-
-
Zavodszky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
-
20
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain AN. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 2003;46: 499-511.
-
(2003)
J Med Chem
, vol.46
, pp. 499-511
-
-
Jain, A.N.1
-
21
-
-
0346665839
-
Gaussian docking functions
-
McGann MR, Almond HR, Nicholls A, Grant JA, Brown FK. Gaussian docking functions. Biopolymers 2003;68:76-90;
-
(2003)
Biopolymers
, vol.68
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
22
-
-
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
-
23
-
-
0037212102
-
LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
Venkatachalam CM, Jiang X, Oldfield T, Waldman M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 2003;21: 289-307.
-
(2003)
J Mol Graph Model
, vol.21
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
24
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins 2003;52: 609-623.
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
25
-
-
0033566211
-
Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
-
Muegge I, Martin YC, Hajduk PJ, Fesik SW. 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
-
26
-
-
0034649618
-
Protein-based virtual screening of chemical databases: 1. Evaluation of different docking/scoring combinations
-
Bissantz C, Folkers G, Rognan D. Protein-based virtual screening of chemical databases: 1. Evaluation of different docking/scoring combinations. J Med Chem 2000;43:4759-4767.
-
(2000)
J Med Chem
, vol.43
, pp. 4759-4767
-
-
Bissantz, C.1
Folkers, G.2
Rognan, D.3
-
27
-
-
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
-
28
-
-
0035846166
-
Are free energy calculations useful in practice?: A comparison with rapid scoring functions for the p38 MAP kinase protein system
-
Pearlman DA, Charifson PS. Are free energy calculations useful in practice?: a comparison with rapid scoring functions for the p38 MAP kinase protein system. J Med Chem 2001;44: 3417-3423.
-
(2001)
J Med Chem
, vol.44
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
29
-
-
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
-
30
-
-
0035811458
-
A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
-
Terp GE, Johansen BN, Christensen IT, Jorgensen FS. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J Med Chem 2001;44:2333-2343.
-
(2001)
J Med Chem
, vol.44
, pp. 2333-2343
-
-
Terp, G.E.1
Johansen, B.N.2
Christensen, I.T.3
Jorgensen, F.S.4
-
31
-
-
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
-
32
-
-
0036136868
-
Consensus scoring for ligand/protein interactions
-
Clark RD, Strizhev A, Leonard JM, Blake JF, Matthew JB. Consensus scoring for ligand/protein interactions. J Mol Graph Model 2002;20:281-295.
-
(2002)
J Mol Graph Model
, vol.20
, pp. 281-295
-
-
Clark, R.D.1
Strizhev, A.2
Leonard, J.M.3
Blake, J.F.4
Matthew, J.B.5
-
33
-
-
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 Engl 2002;41:2644-2676.
-
(2002)
Angew Chem Int Ed Engl
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
34
-
-
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
-
35
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
Charifson PS, Corkery JJ, Murcko MA, Walters WP. Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 1999;42:5100-5109.
-
(1999)
J Med Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
36
-
-
0034791141
-
A virtual high throughput screen for high affinity cytochrome P450cam substrates: Implications for in silico prediction of drug metabolism
-
Keseru GM. A virtual high throughput screen for high affinity cytochrome P450cam substrates: implications for in silico prediction of drug metabolism. J Comput Aided Mol Des 2001;15:649-657.
-
(2001)
J Comput Aided Mol Des
, vol.15
, pp. 649-657
-
-
Keseru, G.M.1
-
37
-
-
0037161605
-
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B
-
Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 2002;45:2213-2221.
-
(2002)
J Med Chem
, vol.45
, pp. 2213-2221
-
-
Doman, T.N.1
McGovern, S.L.2
Witherbee, B.J.3
Kasten, T.P.4
Kurumbail, R.5
Stallings, W.C.6
Connolly, D.T.7
Shoichet, B.K.8
-
38
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink JWM, Murray C, Hartshorn M, Verdonk ML, Cole JC, Taylor R. A new test set for validating predictions of protein-ligand interaction. Proteins 2002;49:457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.M.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
39
-
-
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
-
40
-
-
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
-
41
-
-
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
-
42
-
-
0038185582
-
Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
-
Schulz-Gasch T, Stahl M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J Mol Model 2003;9:47-57.
-
(2003)
J Mol Model
, vol.9
, pp. 47-57
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
43
-
-
0032190489
-
Screening a peptidyl database for potential ligands to proteins with side-chain flexibility
-
Schnecke V, Swanson CA, Getzoff ED, Tainer JA, Kuhn LA. Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 1998;33:74-87.
-
(1998)
Proteins
, vol.33
, pp. 74-87
-
-
Schnecke, V.1
Swanson, C.A.2
Getzoff, E.D.3
Tainer, J.A.4
Kuhn, L.A.5
-
44
-
-
0030979125
-
Automatic identification and representation of protein binding sites for molecular docking
-
Ruppert J, Welch W, Jain AN. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci 1997;6:524-533.
-
(1997)
Protein Sci
, vol.6
, pp. 524-533
-
-
Ruppert, J.1
Welch, W.2
Jain, A.N.3
-
45
-
-
0037404468
-
Selection criteria for drug-like compounds
-
Muegge I. Selection criteria for drug-like compounds. Med Res Rev 2003;23:302-321.
-
(2003)
Med Res Rev
, vol.23
, pp. 302-321
-
-
Muegge, I.1
-
46
-
-
0028881975
-
SURFNET a program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995;13:323-330.
-
(1995)
J Mol Graph
, vol.13
, pp. 323-330
-
-
Laskowski, R.A.1
-
47
-
-
0347296066
-
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
-
Bostrom J, Greenwood JR, Gottfries J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 2003;21:449-462.
-
(2003)
J Mol Graph Model
, vol.21
, pp. 449-462
-
-
Bostrom, J.1
Greenwood, J.R.2
Gottfries, J.3
-
48
-
-
0035104129
-
The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase
-
Wurth C, Kessler U, Vogt J, Schulz GE, Folkers G, Scapozza L. The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase. Protein Sci 2001;10:63-73.
-
(2001)
Protein Sci
, vol.10
, pp. 63-73
-
-
Wurth, C.1
Kessler, U.2
Vogt, J.3
Schulz, G.E.4
Folkers, G.5
Scapozza, L.6
-
49
-
-
0037687855
-
Discovery of novel low molecular weight inhibitors of IMPDH via virtual needle screening
-
Pickett SD, Sherborne BS, Wilkinson T, Bennett J, Borkakoti N, Broadhurst M, Hurst D, Kilford I, McKinnell M, Jones PS. Discovery of novel low molecular weight inhibitors of IMPDH via virtual needle screening. Bioorg Med Chem Lett 2003;13:1691-1694.
-
(2003)
Bioorg Med Chem Lett
, vol.13
, pp. 1691-1694
-
-
Pickett, S.D.1
Sherborne, B.S.2
Wilkinson, T.3
Bennett, J.4
Borkakoti, N.5
Broadhurst, M.6
Hurst, D.7
Kilford, I.8
McKinnell, M.9
Jones, P.S.10
-
50
-
-
0038101420
-
Novel dihydrofolate reductase inhibitors: Structure-based versus diversity-based library design and high-throughput synthesis and screening
-
Wyss PC, Gerber P, Hartman PG, Hubschwerlen C, Locher H, Marty HP, Stahl M. Novel dihydrofolate reductase inhibitors: structure-based versus diversity-based library design and high-throughput synthesis and screening. J Med Chem 2003;46:2304-2312.
-
(2003)
J Med Chem
, vol.46
, pp. 2304-2312
-
-
Wyss, P.C.1
Gerber, P.2
Hartman, P.G.3
Hubschwerlen, C.4
Locher, H.5
Marty, H.P.6
Stahl, M.7
|