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Volumn 48, Issue 4, 2008, Pages 747-754

Structure-based virtual screening with supervised consensus scoring: Evaluation of pose prediction and enrichment factors

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DATABASE SYSTEMS; PROTEINS; SUPERVISED LEARNING;

EID: 44449163512     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700464x     Document Type: Article
Times cited : (13)

References (33)
  • 2
    • 0037107887 scopus 로고    scopus 로고
    • Structure-based virtual screening: An overview
    • Lyne, P. D. Structure-based virtual screening: an overview. Drug Discov. Today 2002, 7, 1047-1055.
    • (2002) Drug Discov. Today , vol.7 , pp. 1047-1055
    • Lyne, P.D.1
  • 4
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical library
    • Shoichet, B. K. Virtual screening of chemical library. Nature. 2004, 432, 862-865.
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 5
    • 0033214412 scopus 로고    scopus 로고
    • Exhaustive docking of molecular fragments on protein binding sites with electrostatic solvation
    • Majeux, N.; Scarsi, M.; Apostolakis, J.; Caisch, A. Exhaustive docking of molecular fragments on protein binding sites with electrostatic solvation. Proteins 1999, 37, 88-105.
    • (1999) Proteins , vol.37 , pp. 88-105
    • Majeux, N.1    Scarsi, M.2    Apostolakis, J.3    Caisch, A.4
  • 6
    • 0033536456 scopus 로고    scopus 로고
    • Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model
    • Zou, X.; Yaxiong, S.; Kuntz, I. D. Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model. J. Am. Chem. Soc. 1999, 121, 8033-8043.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 8033-8043
    • Zou, X.1    Yaxiong, S.2    Kuntz, I.D.3
  • 7
    • 0000934205 scopus 로고    scopus 로고
    • SMoG: De novo design method based on simple; fast; and accurate free energy estimates. 1. Methodology and supporting evidence
    • DeWitte, R.; Shakhnovich, E. SMoG: de novo design method based on simple; fast; and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 1996, 118, 11733-11744.
    • (1996) J. Am. Chem. Soc , vol.118 , pp. 11733-11744
    • DeWitte, R.1    Shakhnovich, E.2
  • 8
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP-Potential of mean force describing protein-ligand interactions: I. Generating potential
    • Mitchell, J. B. O.; Laskowski, R. A.; Alexander, A.; Thornton, J. M. BLEEP-Potential of mean force describing protein-ligand interactions: I. Generating potential. J. Comput. Chem. 1999, 20, 1165-1176.
    • (1999) J. Comput. Chem , vol.20 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alexander, A.3    Thornton, J.M.4
  • 9
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 10
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 2000, 295, 337-356.
    • (2000) J. Mol. Biol , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 11
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening accuracy
    • Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 2004, 57, 225-242.
    • (2004) Proteins , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 12
    • 34247261118 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004, 57, 225-242.
    • (2004) Proteins , vol.57 , pp. 225-242
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 13
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of docking performance: Comparative data on docking algorithms. J. Med. Chem. 2004, 56, 558-565.
    • (2004) J. Med. Chem , vol.56 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 15
    • 11144255694 scopus 로고    scopus 로고
    • Evaluation of library ranking efficacy in virtual screening
    • Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 2005, 26, 11-22.
    • (2005) J. Comput. Chem , vol.26 , pp. 11-22
    • Kontoyianni, M.1    Sokol, G.S.2    McClellan, L.M.3
  • 17
    • 34247262566 scopus 로고    scopus 로고
    • Supervised consensus scoring for docking and virtual screening
    • Teramoto, R; Fukunishi, H. Supervised consensus scoring for docking and virtual screening. J. Chem. Inf. Model. 2007, 47, 526-534.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 526-534
    • Teramoto, R.1    Fukunishi, H.2
  • 18
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho, C. J.; Vajda, S. Protein docking along smooth association pathways. Proc. Natl. Acad. Sci. USA 2001, 98, 10636-10641.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2
  • 19
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking sets for molecular docking
    • Huang, N.; Schoichet, K. B.; Irwin, J. J. Benchmarking sets for molecular docking. J. Med. Chem. 2006, 49, 6789-6801.
    • (2006) J. Med. Chem , vol.49 , pp. 6789-6801
    • Huang, N.1    Schoichet, K.B.2    Irwin, J.J.3
  • 20
    • 44449162959 scopus 로고    scopus 로고
    • FlexSIS, Sybyl7.1J; BioSolveIT GmbH: Sankt Augustin, Germany, 2005.
    • FlexSIS, Sybyl7.1J; BioSolveIT GmbH: Sankt Augustin, Germany, 2005.
  • 21
    • 0346996357 scopus 로고    scopus 로고
    • Improvement structure-based virtual screening by multivariate analysis of scoring data
    • Jacobsson, M.; Liden, P.; Stjernschantz, E.; Bostrom, H.; Norinder, U. Improvement structure-based virtual screening by multivariate analysis of scoring data. J. Med. Chem. 2003, 46, 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
  • 22
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2303.
    • (2003) J. Med. Chem , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 23
    • 0030599010 scopus 로고    scopus 로고
    • 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, 470-89.
    • (1996) J. Mol. Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 24
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
    • Rarey, M.; Kramer, B.; Lengauer, T. Evaluation of the FlexX incremental construction algorithm for protein-ligand docking. Proteins 1999, 37, 228-241.
    • (1999) Proteins , vol.37 , pp. 228-241
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 25
    • 0033673508 scopus 로고    scopus 로고
    • A knowledge-based scoring function or protein-ligand interactions: Probing the reference state
    • Muegge, I. A knowledge-based scoring function or protein-ligand interactions: probing the reference state. Perspect. Drug. Discov. Des. 2000, 20, 99-114.
    • (2000) Perspect. Drug. Discov. Des , vol.20 , pp. 99-114
    • Muegge, I.1
  • 26
    • 0001745748 scopus 로고    scopus 로고
    • Effect of ligand volume correction on PMF scoring
    • Muegge, I. Effect of ligand volume correction on PMF scoring. J. Comput. Chem. 2001, 22, 418-425.
    • (2001) J. Comput. Chem , vol.22 , pp. 418-425
    • Muegge, I.1
  • 27
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 28
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligand in receptor complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, R. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligand in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
    • (1997) J. Comput.-Aided Mol. Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, R.R.3    Paolini, G.V.4    Mee, R.P.5
  • 30
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. Random forests. Machine Learning 2001, 45, 5-32.
    • (2001) Machine Learning , vol.45 , pp. 5-32
    • Breiman, L.1
  • 31
    • 0345548657 scopus 로고    scopus 로고
    • Svetnik, V.; Liaw, A.; Tong, C.; Culberson, C.; Sheridan, R.; Feuston, B. Random Forest: A classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Model. 2003, 43, 1947-1958.
    • Svetnik, V.; Liaw, A.; Tong, C.; Culberson, C.; Sheridan, R.; Feuston, B. Random Forest: A classification and regression tool for compound classification and QSAR modeling. J. Chem. Inf. Model. 2003, 43, 1947-1958.
  • 32
    • 20444392475 scopus 로고    scopus 로고
    • Using random forest to learn imbalanced data
    • Technical Report 666; Statistics Department, University of California at Berkeley: Berkeley, CA
    • Chen, C.; Liaw, L.; Breiman, L. Using random forest to learn imbalanced data, Technical Report 666; Statistics Department, University of California at Berkeley: Berkeley, CA, 2004.
    • (2004)
    • Chen, C.1    Liaw, L.2    Breiman, L.3
  • 33
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases: 1. Evaluation of different docking/scoring combinations
    • Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases: 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
    • (2000) J. Med. Chem , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3


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