-
1
-
-
0018165127
-
Computer analysis of protein-protein interaction
-
Wodak, S. J.; Janin, J. Computer analysis of protein-protein interaction. J. Mol. Biol. 1978, 124, 323-342.
-
(1978)
J. Mol. Biol.
, vol.124
, pp. 323-342
-
-
Wodak, S.J.1
Janin, J.2
-
2
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. 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
-
-
0022993246
-
Docking flexible ligands to macromolecular receptors by molecular shape
-
DesJarlais, R. L.; Sheridan, R. P.; Dixon, J. S.; Kuntz, I. D.; Venkataraghavan, R. Docking flexible ligands to macromolecular receptors by molecular shape. J. Med. Chem. 1986, 29, 2149-2153.
-
(1986)
J. Med. Chem.
, vol.29
, pp. 2149-2153
-
-
Desjarlais, R.L.1
Sheridan, R.P.2
Dixon, J.S.3
Kuntz, I.D.4
Venkataraghavan, R.5
-
4
-
-
0023936327
-
Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
-
DesJarlais, R. L.; Sheridan, R. P.; Seibel, G. L.; Dixon, J. S.; Kuntz, I. D. et al. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 1988, 31, 722-729.
-
(1988)
J. Med. Chem.
, vol.31
, pp. 722-729
-
-
Desjarlais, R.L.1
Sheridan, R.P.2
Seibel, G.L.3
Dixon, J.S.4
Kuntz, I.D.5
-
5
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. 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
-
6
-
-
0029243162
-
New molecular shape descriptors: Application in database screening
-
Good, A. C.; Ewing, T. J.; Gschwend, D. A.; Kuntz, I. D. New molecular shape descriptors: Application in database screening. J. Comput.-Aided Mol. Des. 1995, 9, 1-12.
-
(1995)
J. Comput.-Aided Mol. Des.
, vol.9
, pp. 1-12
-
-
Good, A.C.1
Ewing, T.J.2
Gschwend, D.A.3
Kuntz, I.D.4
-
7
-
-
0025151192
-
Computerized selection of potential DNA binding compounds
-
Grootenhuis, P. D.; Kollman, P. A.; Seibel, G. L.; DesJarlais, R. L.; Kuntz, I. D. Computerized selection of potential DNA binding compounds. Anticancer Drug Des. 1990, 5, 237-242.
-
(1990)
Anticancer Drug Des.
, vol.5
, pp. 237-242
-
-
Grootenhuis, P.D.1
Kollman, P.A.2
Seibel, G.L.3
Desjarlais, R.L.4
Kuntz, I.D.5
-
8
-
-
0030120054
-
Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal
-
Gschwend, D. A.; Kuntz, I. D. Orientational sampling and rigid-body minimization in molecular docking revisited: On-the-fly optimization and degeneracy removal. J. Comput.-Aided Mol. Des. 1996, 10, 123-132.
-
(1996)
J. Comput.-Aided Mol. Des.
, vol.10
, pp. 123-132
-
-
Gschwend, D.A.1
Kuntz, I.D.2
-
9
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. Molecular docking to ensembles of protein structures. J. Mol. Biol. 1997, 266, 424-440.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.1
Kuntz, I.D.2
Oshiro, C.M.3
-
10
-
-
0035865951
-
Design, docking, and evaluation of multiple libraries against multiple targets
-
Lamb, M. L.; Burdick, K. W.; Toba, S.; Young, M. M.; Skillman, A. G. et al. Design, docking, and evaluation of multiple libraries against multiple targets. Proteins 2001, 42, 296-318.
-
(2001)
Proteins
, vol.42
, pp. 296-318
-
-
Lamb, M.L.1
Burdick, K.W.2
Toba, S.3
Young, M.M.4
Skillman, A.G.5
-
11
-
-
0026694615
-
Automated site-directed drug design using molecular lattices
-
Lewis, R. A.; Roe, D. C.; Huang, C.; Ferrin, T. E.; Langridge, R. et al. Automated site-directed drug design using molecular lattices. J. Mol. Graph. 1992, 10, 66-78, 106.
-
(1992)
J. Mol. Graph.
, vol.10
, pp. 66-78
-
-
Lewis, R.A.1
Roe, D.C.2
Huang, C.3
Ferrin, T.E.4
Langridge, R.5
-
12
-
-
0032840569
-
DREAM++: Flexible docking program for virtual combinatorial libraries
-
Makino, S.; Ewing, T. J.; Kuntz, I. D. DREAM++: Flexible docking program for virtual combinatorial libraries. J. Comput.-Aided Mol. Des. 1999, 13, 513-532.
-
(1999)
J. Comput.-Aided Mol. Des.
, vol.13
, pp. 513-532
-
-
Makino, S.1
Ewing, T.J.2
Kuntz, I.D.3
-
13
-
-
0027379219
-
Orientational sampling and rigid-body minimization in molecular docking
-
Meng, E. C.; Gschwend, D. A.; Blaney, J. M.; Kuntz, I. D. Orientational sampling and rigid-body minimization in molecular docking. Proteins 1993, 17, 266-278.
-
(1993)
Proteins
, vol.17
, pp. 266-278
-
-
Meng, E.C.1
Gschwend, D.A.2
Blaney, J.M.3
Kuntz, I.D.4
-
14
-
-
0027385177
-
Matching chemistry and shape in molecular docking
-
Shoichet, B. K.; Kuntz, I. D. Matching chemistry and shape in molecular docking. Protein Eng. 1993, 6, 723-732.
-
(1993)
Protein Eng.
, vol.6
, pp. 723-732
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
15
-
-
0032939345
-
Ligand solvation in molecular docking
-
Shoichet, B. K.; Leach, A. R.; Kuntz, I. D. Ligand solvation in molecular docking. Proteins 1999, 34, 4-16.
-
(1999)
Proteins
, vol.34
, pp. 4-16
-
-
Shoichet, B.K.1
Leach, A.R.2
Kuntz, I.D.3
-
16
-
-
0027522358
-
Structure-based discovery of inhibitors of thymidylate synthase
-
Shoichet, B. K.; Stroud, R. M.; Santi, D. V.; Kuntz, I. D.; Perry, K. M. Structure-based discovery of inhibitors of thymidylate synthase. Science 1993, 259, 1445-1450.
-
(1993)
Science
, vol.259
, pp. 1445-1450
-
-
Shoichet, B.K.1
Stroud, R.M.2
Santi, D.V.3
Kuntz, I.D.4
Perry, K.M.5
-
17
-
-
13344275187
-
Molecular docking programs successfully predict the binding of β-lactamase inhibitory protein to TEM-1 β-lactamase
-
Strynadka, N. C.; Eisenstein, M.; Katchalski-Katzir, E.; Shoichet, B. K.; Kuntz, I. D. et al. Molecular docking programs successfully predict the binding of β-lactamase inhibitory protein to TEM-1 β-lactamase. Nat. Struct. Biol. 1996, 3, 233-239.
-
(1996)
Nat. Struct. Biol.
, vol.3
, pp. 233-239
-
-
Strynadka, N.C.1
Eisenstein, M.2
Katchalski-Katzir, E.3
Shoichet, B.K.4
Kuntz, I.D.5
-
18
-
-
0032196541
-
Combi-DOCK: Structure-based combinatorial docking and library design
-
Sun, Y.; Ewing, T. J.; Skillman, A. G.; Kuntz, I. D. Combi-DOCK: Structure-based combinatorial docking and library design. J. Comput.-Aided Mol. Des. 1998, 12, 597-604.
-
(1998)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 597-604
-
-
Sun, Y.1
Ewing, T.J.2
Skillman, A.G.3
Kuntz, I.D.4
-
19
-
-
0033168443
-
Flexible ligand docking: A multistep strategy approach
-
Wang, J.; Kollman, P. A.; Kuntz, I. D. Flexible ligand docking: A multistep strategy approach. Proteins 1999, 36, 1-19.
-
(1999)
Proteins
, vol.36
, pp. 1-19
-
-
Wang, J.1
Kollman, P.A.2
Kuntz, I.D.3
-
20
-
-
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
-
22
-
-
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
-
23
-
-
0036355265
-
Design and implementation of high throughput screening assays
-
Human Press, Inc.: Totawa, NJ
-
Macarron, R.; Hertzberg, R. P. Design and Implementation of High Throughput Screening Assays. High Throughput Screening Methods and Protocols; Human Press, Inc.: Totawa, NJ, 2002; pp 1-29.
-
(2002)
High Throughput Screening Methods and Protocols
, pp. 1-29
-
-
Macarron, R.1
Hertzberg, R.P.2
-
24
-
-
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
-
25
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. 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
-
26
-
-
0030111106
-
Molecular docking towards drug discovery
-
Gschwend, D. A.; Good, A. C.; Kuntz, I. D. Molecular docking towards drug discovery. J. Mol. Recognit. 1988, 9, 175-186.
-
(1988)
J. Mol. Recognit.
, vol.9
, pp. 175-186
-
-
Gschwend, D.A.1
Good, A.C.2
Kuntz, I.D.3
-
27
-
-
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
-
28
-
-
0038185582
-
Binding site characteristics in structure-based vistual screening: Evaluation of current docking tools
-
Schulz-Gasch, T.; Stahl, M. Binding site characteristics in structure-based vistual 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
-
29
-
-
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
-
30
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola, E.; Walters, W. P.; Charifson, P. S. 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
-
31
-
-
0031804609
-
Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
-
Wlodawer, A.; Vondrasek, J. Inhibitors of HIV-1 protease: A major success of structure-assisted drug design. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 249-284.
-
(1998)
Annu. Rev. Biophys. Biomol. Struct.
, vol.27
, pp. 249-284
-
-
Wlodawer, A.1
Vondrasek, J.2
-
32
-
-
0035415662
-
Protein tyrosine phosphatases: Prospects for therapeutics
-
Zhang, Z. Protein tyrosine phosphatases: prospects for therapeutics. Curr. Opin. Chem. Biol. 2001, 5, 416-423.
-
(2001)
Curr. Opin. Chem. Biol.
, vol.5
, pp. 416-423
-
-
Zhang, Z.1
-
33
-
-
0026102830
-
Thrombin structure and function: Why thrombin is the primary target for anti-thrombotics
-
Fenton, J.; Ofosu, F.; Moon, D.; Maraganore, J. Thrombin structure and function: Why thrombin is the primary target for anti-thrombotics. Blood Coagulation Fibrinolysis 1991, 2, 69-75.
-
(1991)
Blood Coagulation Fibrinolysis
, vol.2
, pp. 69-75
-
-
Fenton, J.1
Ofosu, F.2
Moon, D.3
Maraganore, J.4
-
34
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N. et al. 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
-
35
-
-
0029824928
-
Regulation and role of urokinase plasminogen activator in vascular remodelling
-
Tkachuk, V.; Stepanova, V.; Little, P. J.; Bobik, A. Regulation and role of urokinase plasminogen activator in vascular remodelling. Clin. Exp. Pharmacol. Physiol. 1996, 23, 759-765.
-
(1996)
Clin. Exp. Pharmacol. Physiol.
, vol.23
, pp. 759-765
-
-
Tkachuk, V.1
Stepanova, V.2
Little, P.J.3
Bobik, A.4
-
36
-
-
0030788411
-
The urokinase-type plasminogen activator system in cancer metastasis: A review
-
Andreasen, P. A.; Kjoller, L.; Christensen, L.; Duffy, M. J. The urokinase-type plasminogen activator system in cancer metastasis: A review. Int. J. Cancer 1997, 72, 1-22.
-
(1997)
Int. J. Cancer
, vol.72
, pp. 1-22
-
-
Andreasen, P.A.1
Kjoller, L.2
Christensen, L.3
Duffy, M.J.4
-
37
-
-
0034657792
-
Structure-directed discovery of potent nonpeptidic inhibitors of human urokinase that access a novel binding subsite
-
Nienaber, V. L.; Davidson, D.; Edalji, R.; Giranda, V. L.; Klinghofer, V. et al. Structure-directed discovery of potent nonpeptidic inhibitors of human urokinase that access a novel binding subsite. Structure Fold. Des. 2000, 8, 553-563.
-
(2000)
Structure Fold. Des.
, vol.8
, pp. 553-563
-
-
Nienaber, V.L.1
Davidson, D.2
Edalji, R.3
Giranda, V.L.4
Klinghofer, V.5
-
38
-
-
0028057975
-
Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors
-
Lam, P. Y.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y. et al. Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 1994, 263, 380-384.
-
(1994)
Science
, vol.263
, pp. 380-384
-
-
Lam, P.Y.1
Jadhav, P.K.2
Eyermann, C.J.3
Hodge, C.N.4
Ru, Y.5
-
39
-
-
0034629107
-
2-(Oxalylamino)-benzoic acid is a general, competitive inhibitor of protein-tyrosine phosphatases
-
Andersen, H. S.; Iversen, L. F.; Jeppesen, C. B.; Branner, S.; Norris, K. et al. 2-(oxalylamino)-benzoic acid is a general, competitive inhibitor of protein-tyrosine phosphatases. J. Biol. Chem. 2000, 275, 7101-7108.
-
(2000)
J. Biol. Chem.
, vol.275
, pp. 7101-7108
-
-
Andersen, H.S.1
Iversen, L.F.2
Jeppesen, C.B.3
Branner, S.4
Norris, K.5
-
40
-
-
0032482311
-
Structural analysis of thrombin complexed with potent inhibitors incorporating a phenyl group as a peptide mimetic and aminopyridines as guanidine substitutes
-
Bone, R.; Lu, T.; Illig, C. R.; Soll, R. M.; Spurlino, J. C. Structural analysis of thrombin complexed with potent inhibitors incorporating a phenyl group as a peptide mimetic and aminopyridines as guanidine substitutes. J. Med. Chem. 1998, 41, 2068-2075.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 2068-2075
-
-
Bone, R.1
Lu, T.2
Illig, C.R.3
Soll, R.M.4
Spurlino, J.C.5
-
41
-
-
2942721004
-
Virtual screening using protein-ligand docking: Avoiding artificial enrichment
-
Verdonk, M. L.; Berdini, V.; Hartshorn, M. J.; Mooij, W. T.; Murray, C. W. et al. Virtual screening using protein-ligand docking: avoiding artificial enrichment. J. Chem. Inf. Comput. Sci. 2004, 44, 793-806.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 793-806
-
-
Verdonk, M.L.1
Berdini, V.2
Hartshorn, M.J.3
Mooij, W.T.4
Murray, C.W.5
-
42
-
-
0346731233
-
Multiple active site corrections for docking and virtual screening
-
Vigers, G. P.; Rizzi, J. P. Multiple active site corrections for docking and virtual screening. J. Med. Chem. 2004, 47, 80-89.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 80-89
-
-
Vigers, G.P.1
Rizzi, J.P.2
-
43
-
-
13944271531
-
-
note
-
Compounds containing atoms other than H, Li, B, C, N, O, F, Na, Mg, S, Cl, K, Ca, Br, and I were excluded. Molecular weight was retricted to the range 200-600. Compounds containing α-halo carbonyls, isocyanates, sulfonylhalides, acid halides, aldehydes, anhydrides, polyethers, 4 or more fused phenyl rings, 2 or more nitro groups, or polyfluorinated compounds were excluded.
-
-
-
-
44
-
-
13944263358
-
-
MDDR, http://www.mdl.com/products/knowledge/drug_data_ report/index.jsp.
-
-
-
-
45
-
-
0031024171
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 1997, 23, 3-25.
-
(1997)
Adv. Drug Deliv. Rev.
, vol.23
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
46
-
-
0001797110
-
Rapid generation of high quality approximate 3D molecular structures
-
Pearlman, R. Rapid generation of high quality approximate 3D molecular structures. Chem. Des. Auto. News 1987, 2, 1-6.
-
(1987)
Chem. Des. Auto. News
, vol.2
, pp. 1-6
-
-
Pearlman, R.1
-
47
-
-
31444452744
-
Automatic generation of 3D atomic coordinates for organic molecules
-
Sadowski, J.; Rudolph, C.; Gasteiger, J. Automatic generation of 3D atomic coordinates for organic molecules. Tetrahedron Comput. Methodol. 1990, 3, 537-547.
-
(1990)
Tetrahedron Comput. Methodol.
, vol.3
, pp. 537-547
-
-
Sadowski, J.1
Rudolph, C.2
Gasteiger, J.3
-
48
-
-
0036560521
-
Combinatorial informatics in the post-genomics era
-
Agrafiotis, D. K.; Lobanov, V. S.; Salemme, F. R. Combinatorial informatics in the post-genomics era. Nature Rev. Drug Disc. 2002, 1, 337-346.
-
(2002)
Nature Rev. Drug Disc.
, vol.1
, pp. 337-346
-
-
Agrafiotis, D.K.1
Lobanov, V.S.2
Salemme, F.R.3
-
49
-
-
0026780930
-
A multiple-start Monte Carlo docking method
-
Hart, T. N.; Read, R. J. A multiple-start Monte Carlo docking method. Proteins 1992, 13, 206-222.
-
(1992)
Proteins
, vol.13
, pp. 206-222
-
-
Hart, T.N.1
Read, R.J.2
-
50
-
-
0031297617
-
Critical evaluation of the research docking program for the CASP2 challenge
-
Hart, T. N.; Ness, S. R.; Read, R. J. Critical evaluation of the research docking program for the CASP2 challenge. Proteins 1997, 29(S1), 205-209.
-
(1997)
Proteins
, vol.29
, Issue.S1
, pp. 205-209
-
-
Hart, T.N.1
Ness, S.R.2
Read, R.J.3
-
51
-
-
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
-
52
-
-
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. 1998, 261, 470-489.
-
(1998)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
53
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; 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
-
54
-
-
0027159949
-
The molecular surface package
-
Connolly, M. L. The molecular surface package. J. Mol. Graph. 1993, 11, 139-141.
-
(1993)
J. Mol. Graph.
, vol.11
, pp. 139-141
-
-
Connolly, M.L.1
-
55
-
-
1642310340
-
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
-
Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L. et al. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 2004, 47, 1750-1759.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
-
56
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J. et al. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
-
57
-
-
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
-
58
-
-
0035438402
-
How does consensus scoring work for virtual library screening? An idealized computer experiment
-
Wang, R.; Wang, S. How does consensus scoring work for virtual library screening? An idealized computer experiment. J. Chem. Inf. Comput. Sci. 2001, 41, 1422-1426.
-
(2001)
J. Chem. Inf. Comput. Sci.
, vol.41
, pp. 1422-1426
-
-
Wang, R.1
Wang, S.2
-
59
-
-
0028943182
-
Monte Carlo docking with ubiquitin
-
Cummings, M. D.; Hart, T. N.; Read, R. J. Monte Carlo docking with ubiquitin. Protein Sci. 1995, 4, 885-899.
-
(1995)
Protein Sci.
, vol.4
, pp. 885-899
-
-
Cummings, M.D.1
Hart, T.N.2
Read, R.J.3
-
60
-
-
0032525194
-
Fragment-based modeling of NAD binding to the catalytic subunits of diphtheria and pertussis toxins
-
Cummings, M. D.; Hart, T. N.; Read, R. J. Fragment-based modeling of NAD binding to the catalytic subunits of diphtheria and pertussis toxins. Proteins 1998, 31, 282-298.
-
(1998)
Proteins
, vol.31
, pp. 282-298
-
-
Cummings, M.D.1
Hart, T.N.2
Read, R.J.3
-
61
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C. et al. A new test set for validating predictions of protein-ligand interaction. Proteins: Struct., Funct., Genet. 2002, 49, 457-471.
-
(2002)
Proteins: Struct., Funct., Genet.
, vol.49
, pp. 457-471
-
-
Nissink, J.W.M.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
-
62
-
-
0025785057
-
Protein docking and complementarity
-
Shoichet, B. K.; Kuntz, I. D. Protein docking and complementarity. J. Mol. Biol. 1991, 221, 327-346.
-
(1991)
J. Mol. Biol.
, vol.221
, pp. 327-346
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
63
-
-
2942706223
-
Assessment of docking poses: Interactions-based accuracy classification (IBAC) versus crystal structure deviations
-
Kroemer, R. T.; Vulpetti, A.; McDonald, J. J.; Rohrer, D. C.; Trosset, J. Y. et al. Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations. J. Chem. Inf. Comput. Sci. 2004, 44, 871-881.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 871-881
-
-
Kroemer, R.T.1
Vulpetti, A.2
McDonald, J.J.3
Rohrer, D.C.4
Trosset, J.Y.5
-
64
-
-
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
|