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Volumn 53, Issue 8, 2013, Pages 1923-1933

SFCscoreRF: A random forest-based scoring function for improved affinity prediction of protein-ligand complexes

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARKING; BINDING ENERGY; COMPLEXATION; DECISION TREES; LIGANDS; PROTEINS; REGRESSION ANALYSIS;

EID: 84883250593     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400120b     Document Type: Article
Times cited : (145)

References (37)
  • 1
    • 84871717368 scopus 로고    scopus 로고
    • Scoring Functions for Protein-Ligand Interactions
    • In; Methods and Principles in Medicinal Chemistry Series; Gohlke, H. Wiley-VCH: Weinheim, Germany, Chapter 12
    • Sotriffer, C. Scoring Functions for Protein-Ligand Interactions. In Protein-Ligand Interactions; Methods and Principles in Medicinal Chemistry Series; Gohlke, H., Ed.; Wiley-VCH: Weinheim, Germany, 2012; Chapter 12, pp 237-263.
    • (2012) Protein-Ligand Interactions , pp. 237-263
    • Sotriffer, C.1
  • 3
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
    • Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C. R. Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go Br. J. Pharmacol. 2008, 153 (Suppl) S7-S26
    • (2008) Br. J. Pharmacol. , vol.153 , Issue.SUPPL.
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 4
    • 66149103553 scopus 로고    scopus 로고
    • Comparative assessment of scoring functions on a diverse test set
    • Cheng, T.; Li, X.; Li, Y.; Liu, Z.; Wang, R. Comparative assessment of scoring functions on a diverse test set J. Chem. Inf. Model. 2009, 49, 1079-1093
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1079-1093
    • Cheng, T.1    Li, X.2    Li, Y.3    Liu, Z.4    Wang, R.5
  • 5
    • 67650097331 scopus 로고    scopus 로고
    • Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
    • Cross, J. B.; Thompson, D. C.; Rai, B. K.; Baber, J. C.; Fan, K. Y.; Hu, Y.; Humblet, C. Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy J. Chem. Inf. Model. 2009, 49, 1455-1474
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1455-1474
    • Cross, J.B.1    Thompson, D.C.2    Rai, B.K.3    Baber, J.C.4    Fan, K.Y.5    Hu, Y.6    Humblet, C.7
  • 7
    • 84883237021 scopus 로고    scopus 로고
    • The Challenge of Affinity Prediction: Scoring functions for Structure-Based Virtual Screening
    • In; Methods and Principles in Medicinal Chemistry Series; Sotriffer, C. Wiley-VCH: Weinheim, Germany, Chapter 7
    • Sotriffer, C.; Matter, H. The Challenge of Affinity Prediction: Scoring functions for Structure-Based Virtual Screening. In Virtual Screening; Methods and Principles in Medicinal Chemistry Series; Sotriffer, C., Ed.; Wiley-VCH: Weinheim, Germany, 2011; Chapter 7, pp 177-221.
    • (2011) Virtual Screening , pp. 177-221
    • Sotriffer, C.1    Matter, H.2
  • 8
    • 52249113723 scopus 로고    scopus 로고
    • SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
    • Sotriffer, C. A.; Sanschagrin, P.; Matter, H.; Klebe, G. SFCscore: Scoring functions for affinity prediction of protein-ligand complexes Proteins 2008, 73, 395-419
    • (2008) Proteins , vol.73 , pp. 395-419
    • Sotriffer, C.A.1    Sanschagrin, P.2    Matter, H.3    Klebe, G.4
  • 9
    • 20444410410 scopus 로고    scopus 로고
    • Virtual screening of molecular databases using a support vector machine
    • Jorissen, R. N.; Gilson, M. K. Virtual screening of molecular databases using a support vector machine J. Chem. Inf. Model. 2005, 45, 549-561
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 549-561
    • Jorissen, R.N.1    Gilson, M.K.2
  • 10
    • 36749002607 scopus 로고    scopus 로고
    • A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming
    • Amini, A.; Shrimpton, P.; Muggleton, S.; Sternberg, M. A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming Proteins 2007, 69, 823-831
    • (2007) Proteins , vol.69 , pp. 823-831
    • Amini, A.1    Shrimpton, P.2    Muggleton, S.3    Sternberg, M.4
  • 11
    • 80053313926 scopus 로고    scopus 로고
    • Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries
    • Li, L.; Wang, B.; Meroueh, S. O. Support vector regression scoring of receptor-ligand complexes for rank-ordering and virtual screening of chemical libraries J. Chem. Inf. Model. 2011, 51, 2132-2138
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2132-2138
    • Li, L.1    Wang, B.2    Meroueh, S.O.3
  • 12
    • 77952825581 scopus 로고    scopus 로고
    • A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
    • Ballester, P. J.; Mitchell, J. B. O. A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking Bioinformatics 2010, 26, 1169-1175
    • (2010) Bioinformatics , vol.26 , pp. 1169-1175
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 13
    • 20444422149 scopus 로고    scopus 로고
    • The PDBbind database: Methodologies and updates
    • Wang, R.; Fang, X.; Lu, Y.; Yang, C.-Y.; Wang, S. The PDBbind database: Methodologies and updates J. Med. Chem. 2005, 48, 4111-4119
    • (2005) J. Med. Chem. , vol.48 , pp. 4111-4119
    • Wang, R.1    Fang, X.2    Lu, Y.3    Yang, C.-Y.4    Wang, S.5
  • 14
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures J. Med. Chem. 2004, 47, 2977-2980
    • (2004) J. Med. Chem. , vol.47 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 17
    • 10344258041 scopus 로고    scopus 로고
    • Targeting the mitogen-activated protein kinase cascade to treat cancer
    • Sebolt-Leopold, J. S.; Herrera, R. Targeting the mitogen-activated protein kinase cascade to treat cancer Nat. Rev. Cancer 2004, 4, 937-947
    • (2004) Nat. Rev. Cancer , vol.4 , pp. 937-947
    • Sebolt-Leopold, J.S.1    Herrera, R.2
  • 19
    • 39449115488 scopus 로고    scopus 로고
    • Mechanism and inhibition of LpxC: An essential zinc-dependent deacetylase of bacterial lipid A synthesis
    • Barb, A. W.; Zhou, P. Mechanism and inhibition of LpxC: An essential zinc-dependent deacetylase of bacterial lipid A synthesis Curr. Pharm. Biotechnol. 2008, 9, 9-15
    • (2008) Curr. Pharm. Biotechnol. , vol.9 , pp. 9-15
    • Barb, A.W.1    Zhou, P.2
  • 24
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. Random forests Mach. Learn. 2001, 45, 5-32
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 26
    • 79961135005 scopus 로고    scopus 로고
    • R Development Core Team. R Foundation for Statistical Computing: Vienna, Austria, ISBN 3-900051-07-0.
    • R Development Core Team. R: A Language and Environment for Statistical Computing; R Foundation for Statistical Computing: Vienna, Austria, 2011; ISBN 3-900051-07-0.
    • (2011) R: A Language and Environment for Statistical Computing
  • 27
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw, A.; Wiener, M. Classification and regression by randomForest R News 2002, 2, 18-22
    • (2002) R News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 29
    • 1642310340 scopus 로고    scopus 로고
    • 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.; Banks, J. L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47, 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
  • 32
    • 77955709186 scopus 로고    scopus 로고
    • Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution
    • Greenwood, J. R.; Calkins, D.; Sullivan, A. P.; Shelley, J. C. Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution J. Comput.-Aided Mol. Des. 2010, 24, 591-604
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 591-604
    • Greenwood, J.R.1    Calkins, D.2    Sullivan, A.P.3    Shelley, J.C.4
  • 33
    • 84857189139 scopus 로고    scopus 로고
    • Epik, version 2.2, Impact, version 5.7, Prime, version 2.3; Schrödinger, LLC: New York, 2011.
    • Schrödinger Suite 2011 Protein Preparation Wizard; Epik, version 2.2, Impact, version 5.7, Prime, version 2.3; Schrödinger, LLC: New York, 2011.
    • Schrödinger Suite 2011 Protein Preparation Wizard
  • 34
    • 80054943835 scopus 로고    scopus 로고
    • DSX: A knowledge-based scoring function for the assessment of protein-ligand complexes
    • Neudert, G.; Klebe, G. DSX: A knowledge-based scoring function for the assessment of protein-ligand complexes J. Chem. Inf. Model. 2011, 51, 2731-2745
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 2731-2745
    • Neudert, G.1    Klebe, G.2
  • 35
    • 78649517318 scopus 로고    scopus 로고
    • Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets
    • Kramer, C.; Gedeck, P. Leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets J. Chem. Inf. Model. 2010, 50, 1961-1969
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 1961-1969
    • Kramer, C.1    Gedeck, P.2
  • 36
    • 80051984855 scopus 로고    scopus 로고
    • Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": Significance for the validation of scoring functions
    • Ballester, P. J.; Mitchell, J. B. O. Comments on "leave-cluster-out cross-validation is appropriate for scoring functions derived from diverse protein data sets": Significance for the validation of scoring functions J. Chem. Inf. Model. 2011, 51, 1739-1741
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1739-1741
    • Ballester, P.J.1    Mitchell, J.B.O.2
  • 37
    • 79955574923 scopus 로고    scopus 로고
    • version 1.5.0.5; Schrödinger, LLC: New York.
    • The PyMOL Molecular Graphics System, version 1.5.0.5; Schrödinger, LLC: New York, 2012.
    • (2012) The PyMOL Molecular Graphics System


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