-
2
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger E., Rodrigo J., Muller P., and Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57 (2004) 225-242
-
(2004)
Proteins
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
3
-
-
0038185582
-
Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
-
Schulz-Gasch T., and Stahl M. Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools. J. Mol. Model (Online). 9 (2003) 47-57
-
(2003)
J. Mol. Model (Online).
, vol.9
, pp. 47-57
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
4
-
-
2442716437
-
Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results
-
Klon A.E., Glick M., Thoma M., Acklin P., and Davies J.W. Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results. J. Med. Chem. 47 (2004) 2743-2749
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2743-2749
-
-
Klon, A.E.1
Glick, M.2
Thoma, M.3
Acklin, P.4
Davies, J.W.5
-
5
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola E., Walters W.P., and Charifson P.S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56 (2004) 235-249
-
(2004)
Proteins
, vol.56
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
6
-
-
1642378145
-
Virtual screening for kinase targets
-
Muegge I., and Enyedy I.J. Virtual screening for kinase targets. Curr. Med. Chem. 11 (2004) 693-707
-
(2004)
Curr. Med. Chem.
, vol.11
, pp. 693-707
-
-
Muegge, I.1
Enyedy, I.J.2
-
7
-
-
13944263886
-
Comparison of automated docking programs as virtual screening tools
-
Cummings M.D., DesJarlais R.L., Gibbs A.C., Mohan V., and Jaeger E.P. Comparison of automated docking programs as virtual screening tools. J. Med. Chem. 48 (2005) 962-976
-
(2005)
J. Med. Chem.
, vol.48
, pp. 962-976
-
-
Cummings, M.D.1
DesJarlais, R.L.2
Gibbs, A.C.3
Mohan, V.4
Jaeger, E.P.5
-
8
-
-
11144255694
-
Evaluation of library ranking efficacy in virtual screening
-
Kontoyianni M., Sokol G.S., and McClellan L.M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 26 (2005) 11-22
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 11-22
-
-
Kontoyianni, M.1
Sokol, G.S.2
McClellan, L.M.3
-
9
-
-
33749260698
-
-
G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head, J. Med. Chem., A critical assessment of docking programs and scoring functions, 2005, ASAP Article, DOI: 10.1021/jm050362n.
-
G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head, J. Med. Chem., A critical assessment of docking programs and scoring functions, 2005, ASAP Article, DOI: 10.1021/jm050362n.
-
-
-
-
10
-
-
33244483907
-
On evaluating molecular-docking methods for pose prediction and enrichment factors
-
Chen H., Lyne P.D., Giordanetto F., Lovell T., and Li J. On evaluating molecular-docking methods for pose prediction and enrichment factors. J. Chem. Inf. Model. 46 (2006) 401-415
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 401-415
-
-
Chen, H.1
Lyne, P.D.2
Giordanetto, F.3
Lovell, T.4
Li, J.5
-
11
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., and Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161 (1982) 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
-
12
-
-
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. 8 (2004) 365-370
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 365-370
-
-
Alvarez, J.C.1
-
13
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., and Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19 (1998) 1639-1662
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
14
-
-
0035025191
-
I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing T.J.M., Skillman S., and Kuntz A.G. I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases,. J. Comput. Aided. Mol. Des. 15 (2001) 411-428
-
(2001)
J. Comput. Aided. Mol. Des.
, vol.15
, pp. 411-428
-
-
Ewing, T.J.M.1
Skillman, S.2
Kuntz, A.G.3
-
15
-
-
77956773039
-
-
J. M. Blaney, and J. S. Dixon, 1.0 eds, Metaphorics, LLC, Mission Viejo, CA.
-
J. M. Blaney, and J. S. Dixon, 1.0 eds, Metaphorics, LLC, Mission Viejo, CA.
-
-
-
-
16
-
-
0026780930
-
A multiple-start Monte Carlo docking method
-
Hart T.N., and Read R.J. A multiple-start Monte Carlo docking method. Proteins 13 (1992) 206-222
-
(1992)
Proteins
, vol.13
, pp. 206-222
-
-
Hart, T.N.1
Read, R.J.2
-
17
-
-
0031297617
-
Critical evaluation of the research docking program for the CASP2 challenge
-
Hart T.N., Ness S.R., and Read R.J. Critical evaluation of the research docking program for the CASP2 challenge. Proteins Suppl 1 (1997) 205-209
-
(1997)
Proteins
, vol.SUPPL. 1
, pp. 205-209
-
-
Hart, T.N.1
Ness, S.R.2
Read, R.J.3
-
18
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M., Kramer B., Lengauer T., and Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261 (1996) 470-489
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
19
-
-
0031181346
-
QXP: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C., and Bohacek R.S. QXP: Powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aided. Mol. Des. 11 (1997) 333-344
-
(1997)
J. Comput. Aided. Mol. Des.
, vol.11
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
20
-
-
0346665839
-
Gaussian docking functions
-
McGann M.R., Almond H.R., Nicholls A., Grant J.A., and Brown F.K. Gaussian docking functions. Biopolymers 68 (2003) 76-90
-
(2003)
Biopolymers
, vol.68
, pp. 76-90
-
-
McGann, M.R.1
Almond, H.R.2
Nicholls, A.3
Grant, J.A.4
Brown, F.K.5
-
21
-
-
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., and Shenkin P.S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47 (2004) 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
-
22
-
-
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., and Banks J.L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 47 (2004) 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
-
23
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G., Willett P., Glen R.C., Leach A.R., and Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267 (1997) 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
-
24
-
-
84986522918
-
ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan R.T., and Kuznetsov M.R. ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15 (1994) 488-506
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 488-506
-
-
Abagyan, R.T.1
Kuznetsov, M.R.2
-
25
-
-
0037212102
-
LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
Venkatachalam C.M., Jiang X., Oldfield T., and Waldman M. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model. 21 (2003) 289-307
-
(2003)
J. Mol. Graph. Model.
, vol.21
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
26
-
-
77956726569
-
-
Chemical Computing Group, Montreal, QC, Canada
-
Chemical Computing Group, Montreal, QC, Canada.
-
-
-
-
27
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking
-
Zavodszky M.I., Sanschagrin P.C., Korde R.S., and Kuhn L.A. Distilling the essential features of a protein surface for improving protein-ligand docking. scoring, and virtual screening, J. Comput. Aided. Mol. Des. 16 (2002) 883-902
-
(2002)
scoring, and virtual screening, J. Comput. Aided. Mol. Des.
, vol.16
, pp. 883-902
-
-
Zavodszky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
-
28
-
-
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. 46 (2003) 499-511
-
(2003)
J. Med. Chem.
, vol.46
, pp. 499-511
-
-
Jain, A.N.1
-
29
-
-
0027379219
-
Orientational sampling and rigid-body minimization in molecular docking
-
Meng E.C., Gschwend D.A., Blaney J.M., and Kuntz I.D. Orientational sampling and rigid-body minimization in molecular docking. Proteins 17 (1993) 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
-
30
-
-
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., and 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. 11 (1997) 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
-
31
-
-
0030076041
-
Placement of medium-sized molecular fragments into active sites of proteins
-
Rarey M., Wefing S., and Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J. Comput. Aided. Mol. Des. 10 (1996) 41-54
-
(1996)
J. Comput. Aided. Mol. Des.
, vol.10
, pp. 41-54
-
-
Rarey, M.1
Wefing, S.2
Lengauer, T.3
-
32
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang R., Lai L., and Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided. Mol. Des. 16 (2002) 11-26
-
(2002)
J. Comput. Aided. Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
33
-
-
0033954256
-
The protein data bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 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
-
34
-
-
0033566211
-
Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
-
Muegge I., Martin Y.C., Hajduk P.J., and Fesik S.W. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J. Med. Chem. 42 (1999) 2498-2503
-
(1999)
J. Med. Chem.
, vol.42
, pp. 2498-2503
-
-
Muegge, I.1
Martin, Y.C.2
Hajduk, P.J.3
Fesik, S.W.4
-
35
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang R., Lu Y., Fang X., and Wang S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 44 (2004) 2114-2125
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
36
-
-
5344237409
-
Assessing the impact of high-performance computing on the drug discovery and development process
-
Scott R.K. Assessing the impact of high-performance computing on the drug discovery and development process. DDT, Biosilico 2 (2004) 175-179
-
(2004)
DDT, Biosilico
, vol.2
, pp. 175-179
-
-
Scott, R.K.1
-
37
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
McGovern S.L., and Shoichet B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 46 (2003) 2895-2907
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
38
-
-
33244475355
-
Screening drug-like compounds by docking to homology models: A systematic study
-
Kairys V., Fernandes M.X., and Gilson M.K. Screening drug-like compounds by docking to homology models: A systematic study. J. Chem. Inf. Model. 46 (2006) 365-379
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 365-379
-
-
Kairys, V.1
Fernandes, M.X.2
Gilson, M.K.3
-
39
-
-
0028501715
-
National Cancer Institute Drug Information System 3D database
-
Milne G.W., Nicklaus M.C., Driscoll J.S., Wang S., and Zaharevitz D. National Cancer Institute Drug Information System 3D database. J. Chem. Inf. Comput. Sci. 34 (1994) 1219-1224
-
(1994)
J. Chem. Inf. Comput. Sci.
, vol.34
, pp. 1219-1224
-
-
Milne, G.W.1
Nicklaus, M.C.2
Driscoll, J.S.3
Wang, S.4
Zaharevitz, D.5
-
40
-
-
2942721004
-
Virtual screening using protein-ligand docking: Avoiding artificial enrichment
-
Verdonk M.L., Berdini V., Hartshorn M.J., Mooij W.T., Murray C.W., Taylor R.D., and Watson P. Virtual screening using protein-ligand docking: Avoiding artificial enrichment. J. Chem. Inf. Comput. Sci. 44 (2004) 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
Taylor, R.D.6
Watson, P.7
-
41
-
-
0037208312
-
Consideration of molecular weight during compound selection in virtual target-based database screening
-
Pan Y., Huang N., Cho S., and MacKerell Jr. A.D. Consideration of molecular weight during compound selection in virtual target-based database screening. J. Chem. Inf. Comput. Sci. 43 (2003) 267-272
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 267-272
-
-
Pan, Y.1
Huang, N.2
Cho, S.3
MacKerell Jr., A.D.4
-
42
-
-
17144385534
-
Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
-
Triballeau N., Acher F., Brabet I., Pin J.P., and Bertrand H.O. Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J. Med. Chem. 48 (2005) 2534-2547
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2534-2547
-
-
Triballeau, N.1
Acher, F.2
Brabet, I.3
Pin, J.P.4
Bertrand, H.O.5
-
43
-
-
0035438401
-
Protocols for bridging the peptide to nonpeptide gap in topological similarity searches
-
Sheridan R.P., Singh S.B., Fluder E.M., and Kearsley S.K. Protocols for bridging the peptide to nonpeptide gap in topological similarity searches. J. Chem. Inf. Comput. Sci. 41 (2001) 1395-1406
-
(2001)
J. Chem. Inf. Comput. Sci.
, vol.41
, pp. 1395-1406
-
-
Sheridan, R.P.1
Singh, S.B.2
Fluder, E.M.3
Kearsley, S.K.4
-
44
-
-
0029294584
-
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
-
Gehlhaar D.K., Verkhivker G.M., Rejto P.A., Sherman C.J., Fogel D.B., Fogel L.J., and Freer S.T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 2 (1995) 317-324
-
(1995)
Chem. Biol.
, vol.2
, pp. 317-324
-
-
Gehlhaar, D.K.1
Verkhivker, G.M.2
Rejto, P.A.3
Sherman, C.J.4
Fogel, D.B.5
Fogel, L.J.6
Freer, S.T.7
-
46
-
-
3342933156
-
Target-biased scoring approaches and expert systems in structure-based virtual screening
-
Jansen J.M., and Martin E.J. Target-biased scoring approaches and expert systems in structure-based virtual screening. Curr. Opin. Chem. Biol. 8 (2004) 359-364
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, pp. 359-364
-
-
Jansen, J.M.1
Martin, E.J.2
-
47
-
-
0346996357
-
Improving structure-based virtual screening by multivariate analysis of scoring data
-
Jacobsson M., Liden P., Stjernschantz E., Bostrom H., and Norinder U. Improving structure-based virtual screening by multivariate analysis of scoring data. J. Med. Chem. 46 (2003) 5781-5789
-
(2003)
J. Med. Chem.
, vol.46
, pp. 5781-5789
-
-
Jacobsson, M.1
Liden, P.2
Stjernschantz, E.3
Bostrom, H.4
Norinder, U.5
-
48
-
-
27444445346
-
PostDOCK: A structural, empirical approach to scoring protein ligand complexes
-
Springer C., Adalsteinsson H., Young M.M., Kegelmeyer P.W., and Roe D.C. PostDOCK: A structural, empirical approach to scoring protein ligand complexes. J. Med. Chem. 48 (2005) 6821-6831
-
(2005)
J. Med. Chem.
, vol.48
, pp. 6821-6831
-
-
Springer, C.1
Adalsteinsson, H.2
Young, M.M.3
Kegelmeyer, P.W.4
Roe, D.C.5
-
49
-
-
23044513878
-
Comparing protein-ligand docking programs is difficult
-
Cole J.C., Murray C.W., Nissink J.W., Taylor R.D., and Taylor R. Comparing protein-ligand docking programs is difficult. Proteins 60 (2005) 325-332
-
(2005)
Proteins
, vol.60
, pp. 325-332
-
-
Cole, J.C.1
Murray, C.W.2
Nissink, J.W.3
Taylor, R.D.4
Taylor, R.5
|