-
1
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
DOI 10.1038/nrd1549
-
Kitchen D et al., Docking and scoring in virtual screening for drug discovery: Methodsand applications, Nat Rev Drug Discov 3(11):935-949, 2004. (Pubitemid 39529931)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.11
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
2
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
DOI 10.1002/prot.10115
-
Halperin I et al., Principles of docking: An overview of search algorithms and a guideto scoring functions, Proteins 47(4):409-443, 2002. (Pubitemid 34614722)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.4
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
3
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
DOI 10.1002/prot.21082
-
Sousa S et al., Protein-ligand docking: Current status and future challenges, Proteins65:15-26, 2006. (Pubitemid 44320611)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.1
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
4
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selectivereceptor flexibility
-
Morris GM et al., AutoDock4 and AutoDockTools4: Automated docking with selectivereceptor flexibility, J Comput Chem 30(16):2785-2791, 2009.
-
(2009)
J Comput Chem
, vol.30
, Issue.16
, pp. 2785-2791
-
-
Morris, G.M.1
-
5
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
DOI 10.1023/A:1011115820450
-
Ewing TJ et al., DOCK 4.0: Search strategies for automated molecular docking offlexible molecule databases, J Comput Aid Mol Des 15:411-428, 2001. (Pubitemid 32452109)
-
(2001)
Journal of Computer-Aided Molecular Design
, vol.15
, Issue.5
, pp. 411-428
-
-
Ewing, T.J.A.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
6
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
DOI 10.1038/sj.bjp.0707515, PII 0707515
-
Moitessier N et al., Towards the development of universal, fast and highly accuratedocking/scoring methods: A long way to go, Brit J Pharmacol 153(S1):S7-S26, 2008. (Pubitemid 351340987)
-
(2008)
British Journal of Pharmacology
, vol.153
, Issue.SUPPL. 1
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
7
-
-
1642540577
-
Evaluation of docking performance: Comparative data on dockingalgorithms
-
DOI 10.1021/jm0302997
-
Kontoyianni M et al., Evaluation of docking performance: Comparative data on dockingalgorithms, J Med Chem 47(3):558-565, 2004. (Pubitemid 38129714)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.3
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
8
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
DOI 10.1006/jmbi.1996.0477
-
Rarey M et al., A fast flexible docking method using an incremental constructionalgorithm, J Mol Biol 261(3):470-489, 1996. (Pubitemid 26335901)
-
(1996)
Journal of Molecular Biology
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
9
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
DOI 10.1002/prot.10465
-
Verdonk M et al., Improved protein-ligand docking using GOLD, Proteins 52(4):609-623, 2003. (Pubitemid 37034158)
-
(2003)
Proteins: Structure, Function and Genetics
, vol.52
, Issue.4
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
10
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng T et al., Comparative assessment of scoring functions on a diverse test set,J Chem Inf Model 49(4):1079-1093, 2009.
-
(2009)
J Chem Inf Model
, vol.49
, Issue.4
, pp. 1079-1093
-
-
Cheng, T.1
-
11
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
DOI 10.1021/jm0203783
-
Wang R, Lu Y, Wang S, Comparative evaluation of 11 scoring functions for moleculardocking, J Med Chem 46(12):2287-2303, 2003. (Pubitemid 36637914)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.12
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
12
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-liganddocking: Recent advances and future directions
-
Huang S et al., Scoring functions and their evaluation methods for protein-liganddocking: Recent advances and future directions, Phys Chem Chem Phys 12(40):12899-12908, 2010.
-
(2010)
Phys Chem Chem Phys
, vol.12
, Issue.40
, pp. 12899-12908
-
-
Huang, S.1
-
13
-
-
79953232769
-
Global free energy scoring functions based on distancedependentatom-type pair descriptors
-
Kramer C, Gedeck P, Global free energy scoring functions based on distancedependentatom-type pair descriptors, J Chem Inf Model 51(3):707-720, 2011.
-
(2011)
J Chem Inf Model
, vol.51
, Issue.3
, pp. 707-720
-
-
Kramer, C.1
Gedeck, P.2
-
14
-
-
77952825581
-
A machine learning approach to predicting protein-ligandbinding affinity with applications to molecular docking
-
Ballester P, Mitchell J, A machine learning approach to predicting protein-ligandbinding affinity with applications to molecular docking, Bioinformatics 26(9):1169,2010.
-
(2010)
Bioinformatics
, vol.26
, Issue.9
, pp. 1169
-
-
Ballester, P.1
Mitchell, J.2
-
15
-
-
0016556021
-
A new approach to manipulator control: The cerebellar model articulationcontroller (CMAC)
-
Albus J, A new approach to manipulator control: The cerebellar model articulationcontroller (CMAC), J Dynam Sys Measurement Control 97:220, 1975.
-
(1975)
J Dynam Sys Measurement Control
, vol.97
, pp. 220
-
-
Albus, J.1
-
16
-
-
20444422149
-
The PDBbind database: Methodologies and updates
-
DOI 10.1021/jm048957q
-
Wang R et al., The PDBbind database: Methodologies and updates, J Med Chem48(12):4111-4119, 2005. (Pubitemid 40800619)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
17
-
-
23444454552
-
The amber biomolecular simulation programs
-
Case D et al., The amber biomolecular simulation programs, J Comput Chem26(16):1668, 2005.
-
(2005)
J Comput Chem
, vol.26
, Issue.16
, pp. 1668
-
-
Case, D.1
-
18
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm witha description of desolvation
-
Jones G et al., Molecular recognition of receptor sites using a genetic algorithm witha description of desolvation, J Mol Biol 245:43-53, 1995.
-
(1995)
J Mol Biol
, vol.245
, pp. 43-53
-
-
Jones, G.1
-
19
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
DOI 10.1006/jmbi.1996.0897
-
Jones G et al., Development and validation of a genetic algorithm for flexible docking,J Mol Biol 267(3):727-748, 1997. (Pubitemid 27170693)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
20
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking witha new scoring function, efficient optimization, and multi-threading
-
Trott O, Olson A, AutoDock Vina: Improving the speed and accuracy of docking witha new scoring function, efficient optimization, and multi-threading, J Comput Chem31(2):455-461, 2010.
-
(2010)
J Comput Chem
, vol.31
, Issue.2
, pp. 455-461
-
-
Trott, O.1
Olson, A.2
-
21
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
DOI 10.1023/A:1016357811882
-
Wang R et al., Further development and validation of empirical scoring functions forstructure-based binding affinity prediction, J Comput Aid Mol Des 16:11-26, 2002. (Pubitemid 34855041)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.1
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
22
-
-
78649517318
-
Leave-cluster-out cross-validation is appropriate for scoringfunctions derived from diverse protein data sets
-
Kramer C, Gedeck P, Leave-cluster-out cross-validation is appropriate for scoringfunctions derived from diverse protein data sets, J Chem Inf Model 50(11):1961-1969,2010.
-
(2010)
J Chem Inf Model
, vol.50
, Issue.11
, pp. 1961-1969
-
-
Kramer, C.1
Gedeck, P.2
-
23
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R et al., Multiple sequence alignment with the Clustal series of programs,Nucleic Acid Res 31(13):3497, 2003.
-
(2003)
Nucleic Acid Res
, vol.31
, Issue.13
, pp. 3497
-
-
Chenna, R.1
|