-
1
-
-
0842349389
-
Novel technologies for virtual screening
-
Lengauer, T.; Lemmen, C.; Rarey, M.; Zimmermann, M. Novel technologies for virtual screening Drug Discovery Today 2004, 9, 27-34
-
(2004)
Drug Discovery Today
, vol.9
, pp. 27-34
-
-
Lengauer, T.1
Lemmen, C.2
Rarey, M.3
Zimmermann, M.4
-
2
-
-
0036007208
-
Virtual screening and fast automated docking methods
-
Schneider, G.; Böhm, H.-J. Virtual screening and fast automated docking methods Drug Discovery Today 2002, 7, 64-70
-
(2002)
Drug Discovery Today
, vol.7
, pp. 64-70
-
-
Schneider, G.1
Böhm, H.-J.2
-
3
-
-
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 Discovery 2004, 3, 935-949
-
(2004)
Nat. Rev. Drug Discovery
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
4
-
-
65549168271
-
Docking-based virtual screening: Recent developments
-
Tuccinardi, T. Docking-based virtual screening: recent developments Comb. Chem. High Throughput Screening 2009, 12, 303-14
-
(2009)
Comb. Chem. High Throughput Screening
, vol.12
, pp. 303-314
-
-
Tuccinardi, T.1
-
5
-
-
65649130829
-
Virtual Screening of Drugs: Score Functions, Docking, and Drug Design
-
Breda, A.; Basso, L. A.; Santos, D. S.; de Azevedo, W. F., Jr. Virtual Screening of Drugs: Score Functions, Docking, and Drug Design Curr. Comput.-Aided Drug Des. 2008, 4, 265-272
-
(2008)
Curr. Comput.-Aided Drug Des.
, vol.4
, pp. 265-272
-
-
Breda, A.1
Basso, L.A.2
Santos, D.S.3
De Azevedo Jr., W.F.4
-
6
-
-
84862845860
-
-
OpenEye Scientific Software, ROCS; Santa Fe, NM. (accessed Mar 08).
-
OpenEye Scientific Software, ROCS; Santa Fe, NM. http://www.eyesopen.com/ rocs (accessed Mar 08, 2012).
-
(2012)
-
-
-
7
-
-
84862866289
-
-
Chemical Computing Group, Molecular Operating Environment MOE, Version 2010.10; Montreal, Quebec, Canada. (accessed Mar 08).
-
Chemical Computing Group, Molecular Operating Environment MOE, Version 2010.10; Montreal, Quebec, Canada. http://www.chemcomp.com (accessed Mar 08, 2012).
-
(2012)
-
-
-
8
-
-
79952262090
-
FRED Pose prediction and virtual screening accuracy
-
McGann, M. FRED Pose prediction and virtual screening accuracy J. Chem. Inf. Model. 2011, 51, 578-596
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 578-596
-
-
McGann, M.1
-
9
-
-
84862866291
-
-
OpenEye Scientific Software, OMEGA; Santa Fe, NM. (accessed Mar 08).
-
OpenEye Scientific Software, OMEGA; Santa Fe, NM. http://www.eyesopen. com/omega (accessed Mar 08, 2012).
-
(2012)
-
-
-
10
-
-
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
-
11
-
-
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, 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
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
-
12
-
-
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.; Pollard, W. T.; Banks, J. L. 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
Pollard, W.T.6
Banks, J.L.7
-
13
-
-
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. Comput.-Aided Mol. Des. 2008, 22, 213-228
-
(2008)
J. Comput.-Aided Mol. Des.
, vol.22
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
14
-
-
18344382014
-
Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
-
Kirchmair, J.; Laggner, C.; Wolber, G.; Langer, T. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms J. Chem. Inf. Model. 2005, 45, 422-430
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 422-430
-
-
Kirchmair, J.1
Laggner, C.2
Wolber, G.3
Langer, T.4
-
15
-
-
33746921247
-
Comparative performance assessment of the conformational model generators omega and catalyst: A large-scale survey on the retrieval of protein-bound ligand conformations
-
Kirchmair, J.; Wolber, G.; Laggner, C.; Langer, T. Comparative performance assessment of the conformational model generators omega and catalyst: a large-scale survey on the retrieval of protein-bound ligand conformations J. Chem. Inf. Model. 2006, 46, 1848-1861
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 1848-1861
-
-
Kirchmair, J.1
Wolber, G.2
Laggner, C.3
Langer, T.4
-
16
-
-
0031560777
-
Contact Area Difference (CAD): A Robust Measure to Evaluate Accuracy of Protein Models
-
Abagyan, R. A.; Totrov, M. M. Contact Area Difference (CAD): A Robust Measure to Evaluate Accuracy of Protein Models J. Mol. Biol. 1997, 268, 678-685
-
(1997)
J. Mol. Biol.
, vol.268
, pp. 678-685
-
-
Abagyan, R.A.1
Totrov, M.M.2
-
17
-
-
77956884637
-
T-Analyst: A program for efficient analysis of protein conformational changes by torsion angles
-
Ai, R.; Fatmi, M. Q.; Chang, C.-E. A. T-Analyst: a program for efficient analysis of protein conformational changes by torsion angles J. Comput.-Aided Mol. Des. 2010, 24, 819-827
-
(2010)
J. Comput.-Aided Mol. Des.
, vol.24
, pp. 819-827
-
-
Ai, R.1
Fatmi, M.Q.2
Chang, C.-E.A.3
-
18
-
-
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.; Giordanetto, J.-Y. T. F.; Cotesta, S.; Mcmartin, C.; Kihlen, M.; Stouten, P. F. W. 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
Giordanetto, J.-Y.T.F.5
Cotesta, S.6
McMartin, C.7
Kihlen, M.8
Stouten, P.F.W.9
-
19
-
-
49449086848
-
An alternative method for the evaluation of docking performance: RSR vs RMSD
-
Yusuf, D.; Davis, A. M.; Kleywegt, G. J.; Schmitt, S. An alternative method for the evaluation of docking performance: RSR vs RMSD J. Chem. Inf. Model. 2008, 48, 1411-1422
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1411-1422
-
-
Yusuf, D.1
Davis, A.M.2
Kleywegt, G.J.3
Schmitt, S.4
-
20
-
-
69549110181
-
GARD: A Generally Applicable Replacement for RMSD
-
Baber, J. C.; Thompson, D. C.; Cross, J. B.; Humblet, C. GARD: A Generally Applicable Replacement for RMSD J. Chem. Inf. Model. 2009, 49, 1889-1900
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1889-1900
-
-
Baber, J.C.1
Thompson, D.C.2
Cross, J.B.3
Humblet, C.4
-
21
-
-
77951987154
-
ConfGen: A conformational search method for efficient generation of bioactive conformers
-
Watts, K. S.; Dalal, P.; Murphy, R. B.; Sherman, W.; Friesner, R. A.; Shelley, J. C. ConfGen: a conformational search method for efficient generation of bioactive conformers J. Chem. Inf. Model. 2010, 50, 534-546
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 534-546
-
-
Watts, K.S.1
Dalal, P.2
Murphy, R.B.3
Sherman, W.4
Friesner, R.A.5
Shelley, J.C.6
-
22
-
-
13744260090
-
Union of all the minimum cycle bases of a graph
-
Vismara, P. Union of all the minimum cycle bases of a graph Electron. J. Combin. 1997, 4, 1-15
-
(1997)
Electron. J. Combin.
, vol.4
, pp. 1-15
-
-
Vismara, P.1
-
23
-
-
84945709831
-
Algorithm 97: Shortest path
-
Floyd, R. Algorithm 97: Shortest path. Commun. ACM 1962, 5
-
(1962)
Commun. ACM
, vol.5
-
-
Floyd, R.1
-
24
-
-
0347296066
-
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
-
Boström, J.; Greenwood, J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations J. Mol. Graphics Modell. 2003, 21, 449-462
-
(2003)
J. Mol. Graphics Modell.
, vol.21
, pp. 449-462
-
-
Boström, J.1
Greenwood, J.R.2
Gottfries, J.3
-
25
-
-
2342586724
-
Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
-
Perola, E.; Charifson, P. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding J. Med. Chem. 2004, 47, 2499-510
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.2
-
26
-
-
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, 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
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
27
-
-
70350501158
-
Conformational sampling for large-scale virtual screening: Accuracy versus ensemble size
-
Griewel, A.; Kayser, O.; Schlosser, J.; Rarey, M. Conformational sampling for large-scale virtual screening: accuracy versus ensemble size J. Chem. Inf. Model. 2009, 49, 2303-2311
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2303-2311
-
-
Griewel, A.1
Kayser, O.2
Schlosser, J.3
Rarey, M.4
-
28
-
-
0001109246
-
A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape
-
Grant, J. A.; Gallardo, M. A.; Pickup, B. T. A fast method of molecular shape comparison: A simple application of a Gaussian description of molecular shape J. Comput. Chem. 1996, 17, 1653-1666
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 1653-1666
-
-
Grant, J.A.1
Gallardo, M.A.2
Pickup, B.T.3
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