메뉴 건너뛰기




Volumn 24, Issue 11, 2013, Pages 1001-1004

Improving the accuracy of pose prediction in molecular docking via structural filtering and conformational clustering

Author keywords

Conformational clustering; Molecular docking; Pose prediction; Structural descriptor

Indexed keywords


EID: 84886085616     PISSN: 10018417     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cclet.2013.06.016     Document Type: Article
Times cited : (9)

References (20)
  • 1
    • 4344632851 scopus 로고    scopus 로고
    • Virtual screening in structure-based drug discovery
    • X. Barril, R.E. Hubbard, and S.D. Morley Virtual screening in structure-based drug discovery Mini Rev. Med. Chem. 4 2004 779 791
    • (2004) Mini Rev. Med. Chem. , vol.4 , pp. 779-791
    • Barril, X.1    Hubbard, R.E.2    Morley, S.D.3
  • 2
    • 84863103941 scopus 로고    scopus 로고
    • Design, synthesis characterization and in vitro biological activity of a series of 3-aryl-6-(bromoarylmethyl)-7H-thiazolo[3,2-b]- 1, 2, 4- triazin-7-one derivatives as the novel acetylcholinesterase inhibitors
    • H. Xu, Z. Jin, and S. Liu Design, synthesis characterization and in vitro biological activity of a series of 3-aryl-6-(bromoarylmethyl)-7H-thiazolo[3,2- b]- 1, 2, 4- triazin-7-one derivatives as the novel acetylcholinesterase inhibitors Chin. Chem. Lett. 23 2012 765 768
    • (2012) Chin. Chem. Lett. , vol.23 , pp. 765-768
    • Xu, H.1    Jin, Z.2    Liu, S.3
  • 3
    • 84879927564 scopus 로고    scopus 로고
    • HAT off: Structure-based identification of drug-like inhibitors of p300 histone acetyltransferase
    • F. Zeng, S. Peng, and L. Li HAT off: structure-based identification of drug-like inhibitors of p300 histone acetyltransferase Acta Pharm. Sin. 48 2013 700 708
    • (2013) Acta Pharm. Sin. , vol.48 , pp. 700-708
    • Zeng, F.1    Peng, S.2    Li, L.3
  • 4
    • 84870443681 scopus 로고    scopus 로고
    • Virtual screening methods as tools for drug lead discovery from large chemical libraries
    • X.H. Ma, F. Zhu, and X. Liu Virtual screening methods as tools for drug lead discovery from large chemical libraries Curr. Med. Chem. 19 2012 5562 5571
    • (2012) Curr. Med. Chem. , vol.19 , pp. 5562-5571
    • Ma, X.H.1    Zhu, F.2    Liu, X.3
  • 5
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • B.K. Shoichet Virtual screening of chemical libraries Nature 432 2004 862 865
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 7
    • 84867757394 scopus 로고    scopus 로고
    • Discovery of novel tubulin inhibitors via structure-based hierarchical virtual screening
    • R. Cao, M. Liu, and M. Yin Discovery of novel tubulin inhibitors via structure-based hierarchical virtual screening J. Chem. Inf. Model. 52 2012 2730 2740
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2730-2740
    • Cao, R.1    Liu, M.2    Yin, M.3
  • 8
    • 33244490820 scopus 로고    scopus 로고
    • Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
    • N. Huang, C. Kalyanaraman, J.J. Irwin, and M.P. Jacobson Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening J. Chem. Inf. Model. 46 2006 243 253
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 243-253
    • Huang, N.1    Kalyanaraman, C.2    Irwin, J.J.3    Jacobson, M.P.4
  • 9
    • 52249104684 scopus 로고    scopus 로고
    • Automated clustering of probe molecules from solvent mapping of protein surfaces: New algorithms applied to hot-spot mapping and structure-based drug design
    • M.G. Lerner, K.L. Meagher, and H.A. Carlson Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design J. Comput. Aided Mol. Des. 22 2008 727 736
    • (2008) J. Comput. Aided Mol. Des. , vol.22 , pp. 727-736
    • Lerner, M.G.1    Meagher, K.L.2    Carlson, H.A.3
  • 10
    • 23844444239 scopus 로고    scopus 로고
    • Hierarchical docking of databases of multiple ligand conformations
    • D.M. Lorber, and B.K. Shoichet Hierarchical docking of databases of multiple ligand conformations Curr. Top. Med. Chem. 5 2005 739 749
    • (2005) Curr. Top. Med. Chem. , vol.5 , pp. 739-749
    • Lorber, D.M.1    Shoichet, B.K.2
  • 11
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • L.A. Kelley, S.P. Gardner, and M.J. Sutcliffe An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies Protein Eng. 9 1996 1063 1065
    • (1996) Protein Eng. , vol.9 , pp. 1063-1065
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 12
    • 80053337594 scopus 로고    scopus 로고
    • Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets
    • J.H. Hsieh, S. Yin, and S. Liu Combined application of cheminformatics- and physical force field-based scoring functions improves binding affinity prediction for CSAR data sets J. Chem. Inf. Model. 51 2011 2027 2035
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2027-2035
    • Hsieh, J.H.1    Yin, S.2    Liu, S.3
  • 13
    • 84858023862 scopus 로고    scopus 로고
    • Cheminformatics meets molecular mechanics: A combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening
    • J.H. Hsieh, S. Yin, and X.S. Wang Cheminformatics meets molecular mechanics: a combined application of knowledge-based pose scoring and physical force field-based hit scoring functions improves the accuracy of structure-based virtual screening J. Chem. Inf. Model. 52 2012 16 28
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 16-28
    • Hsieh, J.H.1    Yin, S.2    Wang, X.S.3
  • 14
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • M.D. Eldridge, C.W. Murray, T.R. Auton, G.V. Paolini, and R.P. Mee 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
  • 15
    • 52249113723 scopus 로고    scopus 로고
    • SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
    • C.A. Sotriffer, P. Sanschagrin, H. Matter, and G. Klebe SFCscore: scoring functions for affinity prediction of protein-ligand complexes Proteins 73 2008 395 419
    • (2008) Proteins , vol.73 , pp. 395-419
    • Sotriffer, C.A.1    Sanschagrin, P.2    Matter, H.3    Klebe, G.4
  • 16
    • 80053333972 scopus 로고    scopus 로고
    • CSAR benchmark exercise of 2010: Selection of the protein-ligand complexes
    • J.B. Dunbar Jr., R.D. Smith, and C.Y. Yang CSAR benchmark exercise of 2010: selection of the protein-ligand complexes J. Chem. Inf. Model. 51 2011 2036 2046
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2036-2046
    • Dunbar Jr., J.B.1    Smith, R.D.2    Yang, C.Y.3
  • 17
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • N. Huang, B.K. Shoichet, and J.J. Irwin Benchmarking sets for molecular docking J. Med. Chem. 49 2006 6789 6801
    • (2006) J. Med. Chem. , vol.49 , pp. 6789-6801
    • Huang, N.1    Shoichet, B.K.2    Irwin, J.J.3
  • 18
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • J.J. Irwin, and B.K. Shoichet ZINC - a free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 45 2005 177 182
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 19
    • 70349310248 scopus 로고    scopus 로고
    • Automated site preparation in physics-based rescoring of receptor ligand complexes
    • C.S. Rapp, C. Schonbrun, M.P. Jacobson, C. Kalyanaraman, and N. Huang Automated site preparation in physics-based rescoring of receptor ligand complexes Proteins 77 2009 52 61
    • (2009) Proteins , vol.77 , pp. 52-61
    • Rapp, C.S.1    Schonbrun, C.2    Jacobson, M.P.3    Kalyanaraman, C.4    Huang, N.5
  • 20
    • 4444221565 scopus 로고    scopus 로고
    • UCSF Chimera - A visualization system for exploratory research and analysis
    • E.F. Pettersen, T.D. Goddard, and C.C. Huang UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
    • (2004) J. Comput. Chem. , vol.25 , pp. 1605-1612
    • Pettersen, E.F.1    Goddard, T.D.2    Huang, C.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.