-
2
-
-
79956024935
-
State-of-the-art in ligand-based virtual screening
-
Ripphausen, P., Nisius, B. and Bajorath, J. (2011), 'State-of-the-art in ligand-based virtual screening', Drug Discov. Today Vol. 16, pp. 372-376.
-
(2011)
Drug Discov. Today
, vol.16
, pp. 372-376
-
-
Ripphausen, P.1
Nisius, B.2
Bajorath, J.3
-
3
-
-
77957899529
-
Advances and challenges in protein-ligand docking
-
Huang, S.Y. and Zou, X. (2010), 'Advances and challenges in protein-ligand docking', Int. J. Mol. Sci. Vol. 11, pp. 3016-3034.
-
(2010)
Int. J. Mol. Sci.
, vol.11
, pp. 3016-3034
-
-
Huang, S.Y.1
Zou, X.2
-
5
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
DOI 10.1002/prot.20149
-
Kellenberger, E., Rodrigo, J., Muller, P. and Rognan, D. (2004), 'Comparative evaluation of eight docking tools for docking and virtual screening accuracy', Proteins Vol. 57, pp. 225-242. (Pubitemid 39223729)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.2
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
6
-
-
34249278087
-
Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
-
Rajamani, R. and Good, A.C. (2007), 'Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development', Curr. Opin. Drug Discov. Devel. Vol. 10, pp. 308-315. (Pubitemid 46804927)
-
(2007)
Current Opinion in Drug Discovery and Development
, vol.10
, Issue.3
, pp. 308-315
-
-
Rajamani, R.1
Good, A.C.2
-
7
-
-
0035085038
-
Structure - Activity relationships for a large diverse set of natural, synthetic, and environmental estrogens
-
DOI 10.1021/tx000208y
-
Fang, H., Tong, W., Shi, L.M., Blair, R. et al. (2001), 'Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens', Chem. Res. Toxicol. Vol. 14, pp. 280-294. (Pubitemid 32238488)
-
(2001)
Chemical Research in Toxicology
, vol.14
, Issue.3
, pp. 280-294
-
-
Fang, H.1
Tong, W.2
Shi, L.M.3
Blair, R.4
Perkins, R.5
Branham, W.6
Hass, B.S.7
Xie, Q.8
Dial, S.L.9
Moland, C.L.10
Sheehan, D.M.11
-
8
-
-
53749107256
-
Synthesis, biological evaluation, structural-activity relationship, and docking study for a series of benzoxepin-derived estrogen receptor modulators
-
Barrett, I., Meegan, M.J., Hughes, R.B., Carr, M. et al. (2008), 'Synthesis, biological evaluation, structural-activity relationship, and docking study for a series of benzoxepin-derived estrogen receptor modulators', Bioorg. Med. Chem. Vol. 16, pp. 9554-9573.
-
(2008)
Bioorg. Med. Chem.
, vol.16
, pp. 9554-9573
-
-
Barrett, I.1
Meegan, M.J.2
Hughes, R.B.3
Carr, M.4
-
9
-
-
70349768241
-
Docking and chemoinformatic screens for new ligands and targets
-
Kolb, P., Ferreira, R.S., Irwin, J.J. and Shoichet, B.K. (2009), 'Docking and chemoinformatic screens for new ligands and targets', Curr. Opin. Biotechnol. Vol. 20, pp. 429-436.
-
(2009)
Curr. Opin. Biotechnol.
, vol.20
, pp. 429-436
-
-
Kolb, P.1
Ferreira, R.S.2
Irwin, J.J.3
Shoichet, B.K.4
-
10
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell, D.S., Morris, G.M. and Olson, A.J. (1996), 'Automated docking of flexible ligands: Applications of AutoDock', J. Mol. Recognit. Vol. 9, pp. 1-5. (Pubitemid 126565462)
-
(1996)
Journal of Molecular Recognition
, vol.9
, Issue.1
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
11
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F. et al. (2009), 'AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility', J. Comput. Chem. Vol. 30, pp. 2785-2791.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
-
12
-
-
66449110287
-
DOCK 6: Combining techniques to model RNA-small molecule complexes
-
Lang, P.T., Brozell, S.R., Mukherjee, S., Pettersen, E.F. et al. (2009), 'DOCK 6: Combining techniques to model RNA-small molecule complexes', RNAVol. 15, pp. 1219-1230.
-
(2009)
RNA
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
-
13
-
-
84986518987
-
Molecular docking using shape descriptors
-
Shoichet, B.K., Bodian, D.L. and Kuntz, I.D. (1992), 'Molecular docking using shape descriptors', J. Comput. Chem. Vol. 13, pp. 380-397.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 380-397
-
-
Shoichet, B.K.1
Bodian, D.L.2
Kuntz, I.D.3
-
14
-
-
84986432941
-
Automated docking with grid-based energy evaluation
-
Meng, E.C., Shoichet, B.K. and Kuntz, I.D. (1992), 'Automated docking with grid-based energy evaluation', J. Comput. Chem. Vol. 13, pp. 505-524.
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 505-524
-
-
Meng, E.C.1
Shoichet, B.K.2
Kuntz, I.D.3
-
15
-
-
0035957528
-
FLEXE: Efficient molecular docking considering protein structure variations
-
DOI 10.1006/jmbi.2001.4551
-
Claussen, H., Buning, C., Rarey, M. and Lengauer, T. (2001), 'FlexE: Efficient molecular docking considering protein structure variations', J. Mol. Biol. Vol. 308, pp. 377-395. (Pubitemid 33043576)
-
(2001)
Journal of Molecular Biology
, vol.308
, Issue.2
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
16
-
-
12144289984
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
-
DOI 10.1021/jm0306430
-
Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A. et al. (2004), 'Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy', J. Med. Chem. Vol. 47, pp. 1739-1749. (Pubitemid 38380917)
-
(2004)
Journal of Medicinal Chemistry
, 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
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
DOI 10.1002/prot.10465
-
Verdonk, M.L., Cole, J.C., Hartshorn, M.J., Murray, C.W. et al. (2003), 'Improved protein-ligand docking using GOLD', Proteins Vol. 52, pp. 609-623. (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
-
18
-
-
58149094776
-
RosettaLigand docking with full ligand and receptor flexibility
-
Davis, I.W. and Baker, D. (2009), 'RosettaLigand docking with full ligand and receptor flexibility', J. Mol. Biol. Vol. 385, pp. 381-392.
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 381-392
-
-
Davis, I.W.1
Baker, D.2
-
19
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, snd virtual screening
-
DOI 10.1023/A:1023866311551
-
Zavodszky, M.I., Sanschagrin, P.C., Korde, R.S. and Kuhn, L.A. (2002), 'Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening', J. Comput. Aided Mol. Des. Vol. 16, pp. 883-902. (Pubitemid 36701524)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.12
, pp. 883-902
-
-
Zavodsky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
-
20
-
-
67650236889
-
Scoring ligand similarity in structure-based virtual screening
-
Zavodszky, M.I., Rohatgi, A., Van Voorst, J.R., Yan, H. et al. (2009), 'Scoring ligand similarity in structure-based virtual screening', J. Mol. Recognit. Vol. 22, pp. 280-292.
-
(2009)
J. Mol. Recognit.
, vol.22
, pp. 280-292
-
-
Zavodszky, M.I.1
Rohatgi, A.2
Van Voorst, J.R.3
Yan, H.4
-
21
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
DOI 10.1021/jm020406h
-
Jain, A.N. (2003), 'Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine', J. Med. Chem. Vol. 46, pp. 499-511. (Pubitemid 36182752)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.4
, pp. 499-511
-
-
Jain, A.N.1
-
22
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
DOI 10.1002/prot.21214
-
Huang, S.Y. and Zou, X. (2007), 'Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking', Proteins Vol. 66, pp. 399-421. (Pubitemid 46053470)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.2
, pp. 399-421
-
-
Huang, S.-Y.1
Zou, X.2
-
23
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G.L., Andrews, C.W., Capelli, A.M., Clarke, B. et al. (2006), 'A critical assessment of docking programs and scoring functions', J. Med. Chem. Vol. 49, pp. 5912-5931. (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
24
-
-
23844555629
-
Consensus scoring criteria for improving enrichment in virtual screening
-
DOI 10.1021/ci050034w
-
Yang, J.M., Chen, Y.F., Shen, T.W., Kristal, B.S. et al. (2005), 'Consensus scoring criteria for improving enrichment in virtual screening', J. Chem. Inf. Model. Vol. 45, pp. 1134-1146. (Pubitemid 41156712)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.4
, pp. 1134-1146
-
-
Yang, J.-M.1
Chen, Y.-F.2
Shen, T.-W.3
Kristal, B.S.4
Hsu, D.F.5
-
25
-
-
77956024845
-
Protein kinases: Docking and homology modeling reliability
-
Tuccinardi, T., Botta, M., Giordano, A. and Martinelli, A. (2010), 'Protein kinases: Docking and homology modeling reliability', J. Chem. Inf. Model. Vol. 50, pp. 1432-1441.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1432-1441
-
-
Tuccinardi, T.1
Botta, M.2
Giordano, A.3
Martinelli, A.4
-
26
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
-
DOI 10.1007/s10822-007-9163-6
-
Kirchmair, J., Markt, P., Distinto, S., Wolber, G. et al. (2008), '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. Vol. 22, pp. 213-228. (Pubitemid 351447959)
-
(2008)
Journal of Computer-Aided Molecular Design
, vol.22
, Issue.3-4
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
27
-
-
42649138533
-
Assessment of programs for ligand binding affinity prediction
-
DOI 10.1002/jcc.20893
-
Kim, R. and Skolnick, J. (2008), 'Assessment of programs for ligand binding affinity prediction', J. Comput. Chem. Vol. 29, pp. 1316-1331. (Pubitemid 351594477)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.8
, pp. 1316-1331
-
-
Kim, R.1
Skolnick, J.2
-
28
-
-
76149120388
-
AutoDock vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott, O. and Olson, A.J. (2010), 'AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading', J. Comput. Chem. Vol. 31, pp. 455-461.
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
29
-
-
34249080633
-
Parallel implementation of AutoDock
-
DOI 10.1107/S0021889807011053, PII S0021889807011053
-
Khodade, P., Prabhu, R., Chandra, N., Raha, S. et al. (2007), 'Parallel implementation of AutoDock', J. Appl. Crystallogr. Vol. 40, pp. 598-599. (Pubitemid 46788572)
-
(2007)
Journal of Applied Crystallography
, vol.40
, Issue.3
, pp. 598-599
-
-
Khodade, P.1
Prabhu, R.2
Chandra, N.3
Raha, S.4
Govindarajan, R.5
-
32
-
-
84901034567
-
-
(Accessed 10th March 2011)
-
DeLano, W.L. http://www.pymol.org/ (Accessed 10th March 2011).
-
-
-
DeLano, W.L.1
-
33
-
-
0029878720
-
VMD: Visual molecular dynamics
-
DOI 10.1016/0263-7855(96)00018-5
-
Humphrey, W., Dalke, A. and Schulten, K. (1996), 'VMD: Visual Molecular Dynamics', J. Mol. Graph. Vol. 14, pp. 33-38, 27-38. (Pubitemid 26152973)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.1
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
34
-
-
0028922586
-
LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions
-
Wallace, A.C., Laskowski, R.A. and Thornton, J.M. (1995), 'LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions', Protein Eng. Vol. 8, pp. 127-134.
-
(1995)
Protein Eng.
, vol.8
, pp. 127-134
-
-
Wallace, A.C.1
Laskowski, R.A.2
Thornton, J.M.3
-
35
-
-
79952168691
-
VsLab - An implementation for virtual high-throughput screening using AutoDock and VMD
-
Cerqueira, N.M.F.S.A., Ribeiro, J., Fernandes, P.A. and Ramos, M.J. (2011), 'vsLab - An implementation for virtual high-throughput screening using AutoDock and VMD', Int. J. Quantum Chem. Vol. 111, pp. 1208-1212.
-
(2011)
Int. J. Quantum Chem.
, vol.111
, pp. 1208-1212
-
-
Cerqueira, N.M.F.S.A.1
Ribeiro, J.2
Fernandes, P.A.3
Ramos, M.J.4
-
36
-
-
84901034568
-
-
(Accessed 10th March 2011)
-
DockingServer. http://www.dockingserver.com/web (Accessed 10th March 2011).
-
-
-
-
37
-
-
4444221565
-
UCSF chimera - A visualization system for exploratory research and analysis
-
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S. et al. (2004), 'UCSF Chimera-a visualization system for exploratory research and analysis', J. Comput. Chem. Vol. 25, pp. 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
-
38
-
-
77954261743
-
POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations
-
Porollo, A. and Meller, J. (2010), 'POLYVIEW-MM: Web-based platform for animation and analysis of molecular simulations', Nucleic Acids Res. Vol. 38 (Suppl.), pp. W662-W666.
-
(2010)
Nucleic Acids Res.
, vol.38
, Issue.SUPPL.
-
-
Porollo, A.1
Meller, J.2
-
39
-
-
33846200437
-
Prediction-based fingerprints of protein-protein interactions
-
DOI 10.1002/prot.21248
-
Porollo, A. and Meller, J. (2007), 'Prediction-based fingerprints of protein-protein interactions', Proteins Vol. 66, pp. 630-645. (Pubitemid 46106767)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.3
, pp. 630-645
-
-
Porollo, A.1
Meller, J.2
-
40
-
-
8844262660
-
Principles for modulation of the nuclear receptor superfamily
-
DOI 10.1038/nrd1551
-
Gronemeyer, H., Gustafsson, J.A. and Laudet, V. (2004), 'Principles for modulation of the nuclear receptor superfamily', Nat. Rev. Drug Discov. Vol. 3, pp. 950-964. (Pubitemid 39534319)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.11
, pp. 950-964
-
-
Gronemeyer, H.1
Gustafsson, J.-A.2
Laudet, V.3
-
41
-
-
50649109820
-
Molecular structural characteristics as determinants of estrogen receptor selectivity
-
Agatonovic-Kustrin, S., Turner, J.V. and Glass, B.D. (2008), 'Molecular structural characteristics as determinants of estrogen receptor selectivity', J. Pharm. Biomed. Anal. Vol. 48, pp. 369-375.
-
(2008)
J. Pharm. Biomed. Anal.
, vol.48
, pp. 369-375
-
-
Agatonovic-Kustrin, S.1
Turner, J.V.2
Glass, B.D.3
-
42
-
-
24944455791
-
Molecular responses to xenoestrogens: Mechanistic insights from toxicogenomics
-
DOI 10.1016/j.tox.2005.05.020, PII S0300483X05002428
-
Moggs, J.G. (2005), 'Molecular responses to xenoestrogens: Mechanistic insights from toxicogenomics', Toxicology Vol. 213, pp. 177-193. (Pubitemid 41319744)
-
(2005)
Toxicology
, vol.213
, Issue.3
, pp. 177-193
-
-
Moggs, J.G.1
-
43
-
-
18044382708
-
QSAR Models Using a Large Diverse Set of Estrogens
-
DOI 10.1021/ci000066d
-
Shi, L.M., Fang, H., Tong, W., Wu, J. et al. (2001), 'QSAR models using a large diverse set of estrogens', J. Chem. Inf. Comput. Sci. Vol. 41, pp. 186-195. (Pubitemid 33645689)
-
(2001)
Journal of Chemical Information and Computer Sciences
, vol.41
, Issue.1
, pp. 186-195
-
-
Shi, L.M.1
Fang, H.2
Tong, W.3
Wu, J.4
Perkins, R.5
Blair, R.M.6
Branham, W.S.7
Dial, S.L.8
Moland, C.L.9
Sheehan, D.M.10
-
44
-
-
0036220892
-
Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor
-
Branham, W.S., Dial, S.L., Moland, C.L., Hass, B.S. et al. (2002), 'Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor', J. Nutr. Vol. 132, pp. 658-664. (Pubitemid 34275063)
-
(2002)
Journal of Nutrition
, vol.132
, Issue.4
, pp. 658-664
-
-
Branham, W.S.1
Dial, S.L.2
Moland, C.L.3
Hass, B.S.4
Blair, R.M.5
Fang, H.6
Shi, L.7
Tong, W.8
Perkins, R.G.9
Sheehan, D.M.10
-
45
-
-
0030667676
-
Molecular basis of agonism and antagonism in the oestrogen receptor
-
DOI 10.1038/39645
-
Brzozowski, A.M., Pike, A.C., Dauter, Z., Hubbard, R.E. et al. (1997), 'Molecular basis of agonism and antagonism in the oestrogen receptor', Nature Vol. 389, pp. 753-758. (Pubitemid 27458965)
-
(1997)
Nature
, vol.389
, Issue.6652
, pp. 753-758
-
-
Brzozowski, A.M.1
Pike, A.C.W.2
Dauter, Z.3
Hubbard, R.E.4
Bonn, T.5
Engstrom, O.6
Ohman, L.7
Greene, G.L.8
Gustafsson, J.-A.9
Carlquist, M.10
-
46
-
-
39049168646
-
Understanding mechanisms of toxicity: Insights from drug discovery research
-
DOI 10.1016/j.taap.2007.10.022, PII S0041008X0700467X
-
Houck, K.A. and Kavlock, R.J. (2008), 'Understanding mechanisms of toxicity: Insights from drug discovery research', Toxicol. Appl. Pharmacol. Vol. 227, pp. 163-178. (Pubitemid 351233054)
-
(2008)
Toxicology and Applied Pharmacology
, vol.227
, Issue.2
, pp. 163-178
-
-
Houck, K.A.1
Kavlock, R.J.2
-
47
-
-
66349120133
-
The toxicity data landscape for environmental chemicals
-
Judson, R., Richard, A., Dix, D.J., Houck, K. et al. (2009), 'The toxicity data landscape for environmental chemicals', Environ. Health Perspect. Vol. 117, pp. 685-695.
-
(2009)
Environ. Health Perspect.
, vol.117
, pp. 685-695
-
-
Judson, R.1
Richard, A.2
Dix, D.J.3
Houck, K.4
-
48
-
-
34249846647
-
Artificial intelligence approaches for rational drug design and discovery
-
DOI 10.2174/138161207780765954
-
Duch, W., Swaminathan, K. and Meller, J. (2007), 'Artificial intelligence approaches for rational drug design and discovery', Curr. Pharm. Des. Vol. 13, pp. 1497-1508. (Pubitemid 46863156)
-
(2007)
Current Pharmaceutical Design
, vol.13
, Issue.14
, pp. 1497-1508
-
-
Duch, W.1
Swaminathan, K.2
Meller, J.3
|