-
1
-
-
3242884966
-
High-throughput docking as a source of novel drug leads
-
Alvarez, J. C. High-throughput docking as a source of novel drug leads Curr. Opin. Chem. Biol. 2004, 8 (4) 365-370
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, Issue.4
, pp. 365-370
-
-
Alvarez, J.C.1
-
2
-
-
33745088619
-
Use of an induced fit receptor structure in virtual screening
-
Sherman, W.; Beard, H. S.; Farid, R. Use of an induced fit receptor structure in virtual screening Chem. Biol. Drug. Des. 2006, 67 (1) 83-84
-
(2006)
Chem. Biol. Drug. Des.
, vol.67
, Issue.1
, pp. 83-84
-
-
Sherman, W.1
Beard, H.S.2
Farid, R.3
-
3
-
-
1442351132
-
Protein flexibility in ligand docking and virtual screening to protein kinases
-
Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases J. Mol. Biol. 2004, 337 (1) 209-225
-
(2004)
J. Mol. Biol.
, vol.337
, Issue.1
, pp. 209-225
-
-
Cavasotto, C.N.1
Abagyan, R.A.2
-
4
-
-
21244479779
-
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
-
Barril, X.; Morley, S. D. Unveiling the full potential of flexible receptor docking using multiple crystallographic structures J. Med. Chem. 2005, 48 (13) 4432-4443
-
(2005)
J. Med. Chem.
, vol.48
, Issue.13
, pp. 4432-4443
-
-
Barril, X.1
Morley, S.D.2
-
5
-
-
77951992987
-
Ensemble docking into multiple crystallographically derived protein structures: An evaluation based on the statistical analysis of enrichments
-
Craig, I. R.; Essex, J. W.; Spiegel, K. Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments J. Chem. Inf. Model. 2010, 50 (4) 511-524
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.4
, pp. 511-524
-
-
Craig, I.R.1
Essex, J.W.2
Spiegel, K.3
-
6
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
Huang, S. Y.; Zou, X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking Proteins 2007, 66 (2) 399-421
-
(2007)
Proteins
, vol.66
, Issue.2
, pp. 399-421
-
-
Huang, S.Y.1
Zou, X.2
-
7
-
-
65249157200
-
In pursuit of virtual lead optimization: Pruning ensembles of receptor structures for increased efficiency and accuracy during docking
-
Bolstad, E. S.; Anderson, A. C. In pursuit of virtual lead optimization: pruning ensembles of receptor structures for increased efficiency and accuracy during docking Proteins 2009, 75 (1) 62-74
-
(2009)
Proteins
, vol.75
, Issue.1
, pp. 62-74
-
-
Bolstad, E.S.1
Anderson, A.C.2
-
8
-
-
0034465217
-
A method for including protein flexibility in protein-ligand docking: Improving tools for database mining and virtual screening
-
302-304
-
Broughton, H. B. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening J. Mol. Graph. Model. 2000, 18 (3) 247-257 302-304.
-
(2000)
J. Mol. Graph. Model.
, vol.18
, Issue.3
, pp. 247-257
-
-
Broughton, H.B.1
-
9
-
-
21644473891
-
Representing receptor flexibility in ligand docking through relevant normal modes
-
Cavasotto, C. N.; Kovacs, J. A.; Abagyan, R. A. Representing receptor flexibility in ligand docking through relevant normal modes J. Am. Chem. Soc. 2005, 127 (26) 9632-9640
-
(2005)
J. Am. Chem. Soc.
, vol.127
, Issue.26
, pp. 9632-9640
-
-
Cavasotto, C.N.1
Kovacs, J.A.2
Abagyan, R.A.3
-
10
-
-
0037379786
-
Ligand-induced conformational changes: Improved predictions of ligand binding conformations and affinities
-
Frimurer, T. M.; Peters, G. H.; Iversen, L. F.; Andersen, H. S.; Moller, N. P.; Olsen, O. H. Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities Biophys. J. 2003, 84 (4) 2273-2281
-
(2003)
Biophys. J.
, vol.84
, Issue.4
, pp. 2273-2281
-
-
Frimurer, T.M.1
Peters, G.H.2
Iversen, L.F.3
Andersen, H.S.4
Moller, N.P.5
Olsen, O.H.6
-
11
-
-
77955627131
-
How to choose relevant multiple receptor conformations for virtual screening: A test case of Cdk2 and normal mode analysis
-
Sperandio, O.; Mouawad, L.; Pinto, E.; Villoutreix, B. O.; Perahia, D.; Miteva, M. A. How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis Eur. Biophys. J. 2010, 39 (9) 1365-1372
-
(2010)
Eur. Biophys. J.
, vol.39
, Issue.9
, pp. 1365-1372
-
-
Sperandio, O.1
Mouawad, L.2
Pinto, E.3
Villoutreix, B.O.4
Perahia, D.5
Miteva, M.A.6
-
12
-
-
73949141783
-
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics
-
Armen, R. S.; Chen, J.; Brooks, C. L. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics J. Chem. Theory Comput. 2009, 5 (10) 2909-2923
-
(2009)
J. Chem. Theory Comput.
, vol.5
, Issue.10
, pp. 2909-2923
-
-
Armen, R.S.1
Chen, J.2
Brooks, C.L.3
-
13
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. Soft docking and multiple receptor conformations in virtual screening J. Med. Chem. 2004, 47 (21) 5076-5084
-
(2004)
J. Med. Chem.
, vol.47
, Issue.21
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.2
Costantino, L.3
Shoichet, B.K.4
-
14
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative Curr. Opin. Struct. Biol. 2008, 18 (2) 178-184
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, Issue.2
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
15
-
-
0346665839
-
Gaussian docking functions
-
McGann, M. R.; Almond, H. R.; Nicholls, A.; Grant, J. A.; Brown, F. K. Gaussian docking functions Biopolymers 2003, 68 (1) 76-90
-
(2003)
Biopolymers
, vol.68
, Issue.1
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
16
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28 (1) 235-242
-
(2000)
Nucleic Acids Res.
, vol.28
, Issue.1
, 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
-
17
-
-
1542741046
-
Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring
-
Yoon, S.; Welsh, W. J. Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring J. Chem. Inf. Comput. Sci. 2004, 44 (1) 88-96
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, Issue.1
, pp. 88-96
-
-
Yoon, S.1
Welsh, W.J.2
-
18
-
-
75749093371
-
Recipes for the selection of experimental protein conformations for virtual screening
-
Rueda, M.; Bottegoni, G.; Abagyan, R. Recipes for the selection of experimental protein conformations for virtual screening J. Chem. Inf. Model. 2010, 50 (1) 186-193
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.1
, pp. 186-193
-
-
Rueda, M.1
Bottegoni, G.2
Abagyan, R.3
-
19
-
-
30444442998
-
Protein structures in virtual screening: A case study with CDK2
-
Thomas, M. P.; McInnes, C.; Fischer, P. M. Protein structures in virtual screening: a case study with CDK2 J. Med. Chem. 2006, 49 (1) 92-104
-
(2006)
J. Med. Chem.
, vol.49
, Issue.1
, pp. 92-104
-
-
Thomas, M.P.1
McInnes, C.2
Fischer, P.M.3
-
20
-
-
50249130736
-
Improving database enrichment through ensemble docking
-
Rao, S.; Sanschagrin, P. C.; Greenwood, J. R.; Repasky, M. P.; Sherman, W.; Farid, R. Improving database enrichment through ensemble docking J. Comput. Aided Mol. Des. 2008, 22 (9) 621-627
-
(2008)
J. Comput. Aided Mol. Des.
, vol.22
, Issue.9
, pp. 621-627
-
-
Rao, S.1
Sanschagrin, P.C.2
Greenwood, J.R.3
Repasky, M.P.4
Sherman, W.5
Farid, R.6
-
21
-
-
79956201474
-
Systematic exploitation of multiple receptor conformations for virtual ligand screening
-
Bottegoni, G.; Rocchia, W.; Rueda, M.; Abagyan, R.; Cavalli, A. Systematic exploitation of multiple receptor conformations for virtual ligand screening PLoS One 2011, 6 (5) e18845
-
(2011)
PLoS One
, vol.6
, Issue.5
, pp. 18845
-
-
Bottegoni, G.1
Rocchia, W.2
Rueda, M.3
Abagyan, R.4
Cavalli, A.5
-
22
-
-
84861499934
-
Potential and limitations of ensemble docking
-
Korb, O.; Olsson, T. S.; Bowden, S. J.; Hall, R. J.; Verdonk, M. L.; Liebeschuetz, J. W.; Cole, J. C. Potential and limitations of ensemble docking J. Chem. Inf. Model. 2012, 52 (5) 1262-1274
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.5
, pp. 1262-1274
-
-
Korb, O.1
Olsson, T.S.2
Bowden, S.J.3
Hall, R.J.4
Verdonk, M.L.5
Liebeschuetz, J.W.6
Cole, J.C.7
-
23
-
-
84867760558
-
ALiBERO: Evolving a team of complementary pocket conformations rather than a single leader
-
Rueda, M.; Totrov, M.; Abagyan, R. ALiBERO: Evolving a team of complementary pocket conformations rather than a single leader J. Chem. Inf. Model. 2012, 52 (10) 2705-2714
-
(2012)
J. Chem. Inf. Model.
, vol.52
, Issue.10
, pp. 2705-2714
-
-
Rueda, M.1
Totrov, M.2
Abagyan, R.3
-
24
-
-
77954080572
-
Comparative evaluation of 3D virtual ligand screening methods: Impact of the molecular alignment on enrichment
-
Giganti, D.; Guillemain, H.; Spadoni, J. L.; Nilges, M.; Zagury, J. F.; Montes, M. Comparative evaluation of 3D virtual ligand screening methods: impact of the molecular alignment on enrichment J. Chem. Inf. Model. 2010, 50 (6) 992-1004
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.6
, pp. 992-1004
-
-
Giganti, D.1
Guillemain, H.2
Spadoni, J.L.3
Nilges, M.4
Zagury, J.F.5
Montes, M.6
-
25
-
-
41349110382
-
How to do an evaluation: Pitfalls and traps
-
Hawkins, P. C.; Warren, G. L.; Skillman, A. G.; Nicholls, A. How to do an evaluation: pitfalls and traps J. Comput. Aided Mol. Des. 2008, 22 (3-4) 179-190
-
(2008)
J. Comput. Aided Mol. Des.
, vol.22
, Issue.34
, pp. 179-190
-
-
Hawkins, P.C.1
Warren, G.L.2
Skillman, A.G.3
Nicholls, A.4
-
26
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
McGovern, S. L.; Shoichet, B. K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J. Med. Chem. 2003, 46 (14) 2895-2907
-
(2003)
J. Med. Chem.
, vol.46
, Issue.14
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
27
-
-
84867328344
-
FRED and HYBRID docking performance on standardized datasets
-
McGann, M. FRED and HYBRID docking performance on standardized datasets J. Comput. Aided. Mol. Des. 2012, 26 (8) 897-906
-
(2012)
J. Comput. Aided. Mol. Des.
, vol.26
, Issue.8
, pp. 897-906
-
-
McGann, M.1
-
28
-
-
84865214371
-
Surflex-Dock: Docking benchmarks and real-world application
-
Spitzer, R.; Jain, A. N. Surflex-Dock: Docking benchmarks and real-world application J. Comput. Aided Mol. Des. 2012, 26 (6) 687-699
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, Issue.6
, pp. 687-699
-
-
Spitzer, R.1
Jain, A.N.2
-
29
-
-
84865248640
-
Evaluation of DOCK 6 as a pose generation and database enrichment tool
-
Brozell, S. R.; Mukherjee, S.; Balius, T. E.; Roe, D. R.; Case, D. A.; Rizzo, R. C. Evaluation of DOCK 6 as a pose generation and database enrichment tool J. Comput. Aided Mol. Des. 2012, 26 (6) 749-773
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, Issue.6
, pp. 749-773
-
-
Brozell, S.R.1
Mukherjee, S.2
Balius, T.E.3
Roe, D.R.4
Case, D.A.5
Rizzo, R.C.6
-
30
-
-
33747818007
-
CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.; Liang, J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Res. 2006, 34 (Web Server issue) W116-W118
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
Liang, J.6
-
31
-
-
79751535059
-
POVME: An algorithm for measuring binding-pocket volumes
-
Durrant, J. D.; de Oliveira, C. A.; McCammon, J. A. POVME: an algorithm for measuring binding-pocket volumes J. Mol. Graph. Model. 2011, 29 (5) 773-776
-
(2011)
J. Mol. Graph. Model.
, vol.29
, Issue.5
, pp. 773-776
-
-
Durrant, J.D.1
De Oliveira, C.A.2
McCammon, J.A.3
-
32
-
-
0001528720
-
Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients for Macromolecules
-
Fraczkiewicz, R.; W, B. Exact and Efficient Analytical Calculation of the Accessible Surface Areas and Their Gradients for Macromolecules J. Comput. Chem. 1998, 19 (3) 319-333
-
(1998)
J. Comput. Chem.
, vol.19
, Issue.3
, pp. 319-333
-
-
Fraczkiewicz, R.1
-
33
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25 (13) 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
34
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain, A. N. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine J. Med. Chem. 2003, 46 (4) 499-511
-
(2003)
J. Med. Chem.
, vol.46
, Issue.4
, pp. 499-511
-
-
Jain, A.N.1
-
35
-
-
84986522918
-
ICM - A new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation
-
Abagyan, R.; Totrov, M.; Kusnetsov, D. ICM-a new method for protein modelling and design. Applications to docking and structure prediction from the distorted native conformation J. Comput. Chem. 1994, 15, 488-506
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kusnetsov, D.3
-
36
-
-
0038798604
-
Nuclear hormone receptor targeted virtual screening
-
Schapira, M.; Abagyan, R.; Totrov, M. Nuclear hormone receptor targeted virtual screening J. Med. Chem. 2003, 46 (14) 3045-3059
-
(2003)
J. Med. Chem.
, vol.46
, Issue.14
, pp. 3045-3059
-
-
Schapira, M.1
Abagyan, R.2
Totrov, M.3
-
37
-
-
27544491192
-
ROCR: Visualizing classifier performance in R
-
Sing, T.; Sander, O.; Beerenwinkel, N.; Lengauer, T. ROCR: visualizing classifier performance in R Bioinformatics 2005, 21 (20) 3940-3941
-
(2005)
Bioinformatics
, vol.21
, Issue.20
, pp. 3940-3941
-
-
Sing, T.1
Sander, O.2
Beerenwinkel, N.3
Lengauer, T.4
-
38
-
-
0037806022
-
Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase
-
Birch, L.; Murray, C. W.; Hartshorn, M. J.; Tickle, I. J.; Verdonk, M. L. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase J. Comput. Aided Mol. Des. 2002, 16 (12) 855-869
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, Issue.12
, pp. 855-869
-
-
Birch, L.1
Murray, C.W.2
Hartshorn, M.J.3
Tickle, I.J.4
Verdonk, M.L.5
-
39
-
-
84865224649
-
Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function
-
Schneider, N.; Hindle, S.; Lange, G.; Klein, R.; Albrecht, J.; Briem, H.; Beyer, K.; Claussen, H.; Gastreich, M.; Lemmen, C.; Rarey, M. Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function J. Comput. Aided Mol. Des. 2012, 26 (6) 701-723
-
(2012)
J. Comput. Aided Mol. Des.
, vol.26
, Issue.6
, pp. 701-723
-
-
Schneider, N.1
Hindle, S.2
Lange, G.3
Klein, R.4
Albrecht, J.5
Briem, H.6
Beyer, K.7
Claussen, H.8
Gastreich, M.9
Lemmen, C.10
Rarey, M.11
-
40
-
-
84864264343
-
Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking
-
Mysinger, M. M.; Carchia, M.; Irwin, J. J.; Shoichet, B. K. Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking J. Med. Chem. 2012, 55 (14) 6582-6594
-
(2012)
J. Med. Chem.
, vol.55
, Issue.14
, pp. 6582-6594
-
-
Mysinger, M.M.1
Carchia, M.2
Irwin, J.J.3
Shoichet, B.K.4
-
41
-
-
0034306499
-
Nuclear receptor ligand-binding domains: Three-dimensional structures, molecular interactions and pharmacological implications
-
Bourguet, W.; Germain, P.; Gronemeyer, H. Nuclear receptor ligand-binding domains: three-dimensional structures, molecular interactions and pharmacological implications Trends Pharmacol. Sci. 2000, 21 (10) 381-388
-
(2000)
Trends Pharmacol. Sci.
, vol.21
, Issue.10
, pp. 381-388
-
-
Bourguet, W.1
Germain, P.2
Gronemeyer, H.3
|