메뉴 건너뛰기




Volumn 5, Issue 5, 2011, Pages 497-505

Survey of public domain software for docking simulations and virtual screening

Author keywords

Docking packages; Drug discovery; Oestrogen activity prediction; Oestrogen receptor; SAR; Small molecule docking; Virtual screening; Visualisation of docking poses

Indexed keywords

ESTRADIOL DERIVATIVE; ESTROGEN RECEPTOR ALPHA; LIGAND; PROTEIN;

EID: 84856031509     PISSN: 14739542     EISSN: 14797364     Source Type: Journal    
DOI: 10.1186/1479-7364-5-5-497     Document Type: Review
Times cited : (60)

References (48)
  • 2
    • 79956024935 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 8
    • 53749107256 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 18
    • 58149094776 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 25
    • 77956024845 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 32
    • 84901034567 scopus 로고    scopus 로고
    • (Accessed 10th March 2011)
    • DeLano, W.L. http://www.pymol.org/ (Accessed 10th March 2011).
    • DeLano, W.L.1
  • 33
    • 0029878720 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • (Accessed 10th March 2011)
    • DockingServer. http://www.dockingserver.com/web (Accessed 10th March 2011).
  • 37
    • 4444221565 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 46
    • 39049168646 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.