-
2
-
-
33749513370
-
Scoring functions for protein-ligand docking
-
Jain, A. N. Scoring functions for protein-ligand docking. Curr. Protein Pept Sci. 2006, 7 (5), 407-420.
-
(2006)
Curr. Protein Pept Sci
, vol.7
, Issue.5
, pp. 407-420
-
-
Jain, A.N.1
-
3
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection What can we learn from earlier mistakes?
-
Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection What can we learn from earlier mistakes? J. CAMD 2008, 22 (3), 213-228.
-
(2008)
J. CAMD
, vol.22
, Issue.3
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
4
-
-
84862027743
-
Recognizing pitfalls in virtual screening: A critical review
-
Scior, T.; Bender, A.; Tresadern, G.; Medina-Franco, J. L.; Martínez-Mayorga, K.; Langer, T.; Cuanalo-Contreras, K.; Agrafiotis, D. K. Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf Model 2012, 52 (4), 867-881.
-
(2012)
J. Chem. Inf Model
, vol.52
, Issue.4
, pp. 867-881
-
-
Scior, T.1
Bender, A.2
Tresadern, G.3
Medina-Franco, J.L.4
Martínez-Mayorga, K.5
Langer, T.6
Cuanalo-Contreras, K.7
Agrafiotis, D.K.8
-
5
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren, G.; Andrews, C.; Capelli, A.; Clarke, B.; LaLonde, J. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2005, 49, 5912-5931.
-
(2005)
J. Med. Chem
, vol.49
, pp. 5912-5931
-
-
Warren, G.1
Andrews, C.2
Capelli, A.3
Clarke, B.4
Lalonde, J.5
-
6
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov 2004, 3 (11), 935-949.
-
(2004)
Nat. Rev. Drug Discov
, vol.3
, Issue.11
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
7
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara, P.; Gohlke, H.; Price, D.; Klebe, G.; Brooks, C. I. 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.3
Klebe, G.4
Brooks, C.I.5
-
8
-
-
67650097331
-
Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
-
Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf Model 2009, 49 (6), 1455-1474.
-
(2009)
J. Chem. Inf Model
, vol.49
, Issue.6
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
9
-
-
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: Struct., Funct., Bioinf. 2004, 57 (2), 225-242.
-
(2004)
Proteins: Struct., Funct., Bioinf
, vol.57
, Issue.2
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
10
-
-
0346962971
-
Structural interaction fingerprint (sift): A novel method for analyzing three-dimensional protein-ligand binding interactions
-
Deng, Z.; Chuaqui, C.; Singh, J. Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions. J. Med. Chem. 2003, 47 (2), 337-344.
-
(2003)
J. Med. Chem
, vol.47
, Issue.2
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
11
-
-
33646253652
-
Knowledge-based interaction fingerprint scoring: A simple method for improving the effectiveness of fast scoring functions
-
Mpamhanga, C. P.; Chen, B.; McLay, I. M.; Willett, P. Knowledge-Based Interaction Fingerprint Scoring: A Simple Method for Improving the Effectiveness of Fast Scoring Functions. J. Chem. Inf Model 2006, 46 (2), 686-698.
-
(2006)
J. Chem. Inf Model
, vol.46
, Issue.2
, pp. 686-698
-
-
Mpamhanga, C.P.1
Chen, B.2
McLay, I.M.3
Willett, P.4
-
12
-
-
66249123260
-
APIF: A new interaction fingerprint based on atom pairs and its application to virtual screening
-
Pérez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixidó, J. APIF: A New Interaction Fingerprint Based on Atom Pairs and Its Application to Virtual Screening. J. Chem. Inf Model 2009, 49 (5), 1245-1260.
-
(2009)
J. Chem. Inf Model
, vol.49
, Issue.5
, pp. 1245-1260
-
-
Pérez-Nueno, V.I.1
Rabal, O.2
Borrell, J.I.3
Teixidó, J.4
-
13
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
Marcou, G.; Rognan, D. Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints. J. Chem. Inf. Model. 2006, 47 (1), 195-207.
-
(2006)
J. Chem. Inf. Model
, vol.47
, Issue.1
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
15
-
-
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
-
16
-
-
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.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47 (7), 1739-1749.
-
(2004)
J. Med. Chem
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
17
-
-
84916598331
-
-
Accelrys Software Inc
-
Pipeline Pilot, ver. 8.5, Accelrys Software Inc. 2009.
-
(2009)
Pipeline Pilot Ver. 8.5
-
-
-
18
-
-
78650689245
-
Comprehensive comparison of ligand-based virtual screening tools against the dud data set reveals limitations of current 3d methods
-
Venkatraman, V.; Pérez-Nueno, V. I.; Mavridis, L.; Ritchie, D. W. Comprehensive Comparison of Ligand-Based Virtual Screening Tools Against the DUD Data set Reveals Limitations of Current 3D Methods. J. Chem. Inf. Model. 2010, 50 (12), 2079-2093.
-
(2010)
J. Chem. Inf. Model
, vol.50
, Issue.12
, pp. 2079-2093
-
-
Venkatraman, V.1
Pérez-Nueno, V.I.2
Mavridis, L.3
Ritchied, W.4
-
19
-
-
33244478322
-
Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes
-
Oda, A.; Tsuchida, K.; Takakura, T.; Yamaotsu, N.; Hirono, S. Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes. J. Chem. Inf. Model. 2006, 46, 380.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 380
-
-
Oda, A.1
Tsuchida, K.2
Takakura, T.3
Yamaotsu, N.4
Hirono, S.5
-
20
-
-
33846212271
-
Comparison of shape-matching and docking as virtual screening tools
-
Hawkins, P. C.; Skillman, A. G.; Nicholls, A. Comparison of shape-matching and docking as virtual screening tools. J. Med. Chem. 2007, 50 (1), 74-82.
-
(2007)
J. Med. Chem
, vol.50
, Issue.1
, pp. 74-82
-
-
Hawkins, P.C.1
Skillman, A.G.2
Nicholls, A.3
-
21
-
-
34547673017
-
Comparison of topological, shape, and docking methods in virtual screening
-
McGaughey, G. B.; Sheridan, R. P.; Bayly, C. I.; Culberson, J. C.; Kreatsoulas, C.; Lindsley, S.; Maiorov, V.; Truchon, J. F.; Cornell, W. D. Comparison of topological, shape, and docking methods in virtual screening. J. Chem. Inf Model 2007, 47 (4), 1504-1519.
-
(2007)
J. Chem. Inf Model
, vol.47
, Issue.4
, pp. 1504-1519
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
Culberson, J.C.4
Kreatsoulas, C.5
Lindsley, S.6
Maiorov, V.7
Truchon, J.F.8
Cornell, W.D.9
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