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Volumn 10, Issue , 2009, Pages

A statistical framework to evaluate virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

BOOTSTRAP SIMULATION; EXACT DISTRIBUTION; EXTENSIVE SIMULATIONS; RECEIVER OPERATING CHARACTERISTIC CURVES; STATISTICAL COMPARISONS; STATISTICAL FRAMEWORK; TYPE I ERROR RATE; VIRTUAL SCREENING;

EID: 68949158347     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-225     Document Type: Article
Times cited : (86)

References (36)
  • 1
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • 1360234 15602552 10.1038/nature03197
    • Shoichet BK Virtual screening of chemical libraries Nature 2004, 432(7019):862-5 1360234 15602552 10.1038/nature03197
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 2
    • 53349142711 scopus 로고    scopus 로고
    • Enhancing drug discovery through in silico screening: Strategies to increase true positives retrieval rates
    • 10.2174/092986708785132843 18691055
    • Kirchmair J Distinto S Schuster D Spitzer G Langer T Wolber G Enhancing drug discovery through in silico screening: Strategies to increase true positives retrieval rates Current Medicinal Chemistry 2008, 15(20):2040-53 10.2174/092986708785132843 18691055
    • (2008) Current Medicinal Chemistry , vol.15 , Issue.20 , pp. 2040-2053
    • Kirchmair, J.1    Distinto, S.2    Schuster, D.3    Spitzer, G.4    Langer, T.5    Wolber, G.6
  • 3
    • 4644235643 scopus 로고    scopus 로고
    • Virtual screening in lead discovery and optimization
    • Jain AN Virtual screening in lead discovery and optimization Current Opinion Drug Discovery & Development 2004, 7(4):396-403
    • (2004) Current Opinion Drug Discovery & Development , vol.7 , Issue.4 , pp. 396-403
    • Jain, A.N.1
  • 4
    • 34447275949 scopus 로고    scopus 로고
    • Ligand docking and structure-based virtual screening in drug discovery
    • 10.2174/156802607780906753 17508934
    • Cavasotto CN Orry AJ Ligand docking and structure-based virtual screening in drug discovery Current Topics in Medicinal Chemistry 2007, 7(10):1006-14 10.2174/156802607780906753 17508934
    • (2007) Current Topics in Medicinal Chemistry , vol.7 , Issue.10 , pp. 1006-1014
    • Cavasotto, C.N.1    Orry, A.J.2
  • 5
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • 10.1016/j.drudis.2006.05.012 16793526
    • Klebe G Virtual ligand screening: Strategies, perspectives and limitations Drug Discovery Today 2006, 11(13-14):580-94 10.1016/ j.drudis.2006.05.012 16793526
    • (2006) Drug Discovery Today , vol.11 , Issue.13-14 , pp. 580-594
    • Klebe, G.1
  • 7
    • 23844456151 scopus 로고    scopus 로고
    • Here be dragons: Docking and screening in an uncharted region of chemical space
    • 10.1177/1087057105281047
    • Brenk R Irwin JJ Shoichet BK Here be dragons: Docking and screening in an uncharted region of chemical space Journal Biomolecular Screening 2005, 10(7):667-74 10.1177/1087057105281047
    • (2005) Journal Biomolecular Screening , vol.10 , Issue.7 , pp. 667-674
    • Brenk, R.1    Irwin, J.J.2    Shoichet, B.K.3
  • 8
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • 10.1021/jm001044l
    • Bissantz C Folkers G Rognan D Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations Journal Medicinal Chemistry 2000, 43(25):4759-67 10.1021/ jm001044l
    • (2000) Journal Medicinal Chemistry , vol.43 , Issue.25 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 10
    • 33244483907 scopus 로고    scopus 로고
    • On evaluating molecular-docking methods for pose prediction and enrichment factors
    • 10.1021/ci0503255
    • Chen H Lyne PD Giordanetto F Lovell T Li J On evaluating molecular-docking methods for pose prediction and enrichment factors Journal of Chemical Information Modeling 2006, 46(1):401-15 10.1021/ ci0503255
    • (2006) Journal of Chemical Information Modeling , vol.46 , Issue.1 , pp. 401-415
    • Chen, H.1    Lyne, P.D.2    Giordanetto, F.3    Lovell, T.4    Li, J.5
  • 11
    • 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?
    • 10.1007/s10822-007-9163-6 18196462
    • Kirchmair J Markt P Distinto S Wolber G Langer T Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-what can we learn from earlier mistakes? Journal of Computer-Aided Molecular Design 2008, 22(3-4):213-28 10.1007/s10822-007-9163-6 18196462
    • (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
  • 12
    • 23044513878 scopus 로고    scopus 로고
    • Comparing protein-ligand docking programs is difficult
    • 10.1002/prot.20497 15937897
    • Cole JC Murray CW Nissink JWM Taylor RD Taylor R Comparing protein-ligand docking programs is difficult Proteins 2005, 60(3):325-32 10.1002/prot.20497 15937897
    • (2005) Proteins , vol.60 , Issue.3 , pp. 325-332
    • Cole, J.C.1    Murray, C.W.2    Nissink, J.W.M.3    Taylor, R.D.4    Taylor, R.5
  • 13
    • 41349084852 scopus 로고    scopus 로고
    • Bias, reporting, and sharing: Computational evaluations of docking methods
    • 10.1007/s10822-007-9151-x 18075713
    • Jain AN Bias, reporting, and sharing: Computational evaluations of docking methods Journal of Computer-Aided Molecular Design 2008, 22(3-4):201-12 10.1007/s10822-007-9151-x 18075713
    • (2008) Journal of Computer-Aided Molecular Design , vol.22 , Issue.3-4 , pp. 201-212
    • Jain, A.N.1
  • 16
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem
    • 10.1021/ci600426e
    • Truchon JF Bayly CI Evaluating virtual screening methods: Good and bad metrics for the "early recognition" problem Journal of Chemical Information Modeling 2007, 47:488-508 10.1021/ci600426e
    • (2007) Journal of Chemical Information Modeling , vol.47 , pp. 488-508
    • Truchon, J.F.1    Bayly, C.I.2
  • 17
    • 17144385534 scopus 로고    scopus 로고
    • Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4
    • 10.1021/jm049092j 15801843
    • Triballeau N Acher F Brabet I Pin JP Bertrand HO Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4 Journal of Medicinal Chemistry 2005, 48:2534-47 10.1021/jm049092j 15801843
    • (2005) Journal of Medicinal Chemistry , vol.48 , pp. 2534-4257
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.P.4    Bertrand, H.O.5
  • 19
    • 33646740651 scopus 로고    scopus 로고
    • Parameter estimation for scoring protein-ligand interactions using negative training data
    • 10.1021/jm050040j
    • Pham TA Jain AN Parameter estimation for scoring protein-ligand interactions using negative training data Journal of Medicinal Chemistry 2005, 49:5856-68 10.1021/jm050040j
    • (2005) Journal of Medicinal Chemistry , vol.49 , pp. 5856-5868
    • Pham, T.A.1    Jain, A.N.2
  • 20
    • 33846996344 scopus 로고    scopus 로고
    • Scoring functions and enrichment: A case study on Hsp90
    • 1790905 17257425 10.1186/1471-2105-8-27
    • Konstantinou-Kirtay C Mitchell JBO Lumley JA Scoring functions and enrichment: A case study on Hsp90 BMC Bioinformatics 2007, 8:27 1790905 17257425 10.1186/1471-2105-8-27
    • (2007) BMC Bioinformatics , vol.8 , pp. 27
    • Konstantinou-Kirtay, C.1    Mitchell, J.B.O.2    Lumley, J.A.3
  • 21
    • 43349090139 scopus 로고    scopus 로고
    • A novel hybrid ultrafast shape descriptor method for use in virtual screening
    • 2275267 18282294 10.1186/1752-153X-2-3
    • Cannon EO Nigsch F Mitchell JBO A novel hybrid ultrafast shape descriptor method for use in virtual screening Chemistry Central Journal 2008, 2:3 2275267 18282294 10.1186/1752-153X-2-3
    • (2008) Chemistry Central Journal , vol.2 , pp. 3
    • Cannon, E.O.1    Nigsch, F.2    Mitchell, J.B.O.3
  • 22
    • 41349084852 scopus 로고    scopus 로고
    • Bias, reporting, and sharing: Computational evaluations of docking methods
    • 10.1007/s10822-007-9151-x 18075713
    • Jain AN Bias, reporting, and sharing: Computational evaluations of docking methods Journal of Computer-Aided Molecular Design 2008, 22:201-12 10.1007/s10822-007-9151-x 18075713
    • (2008) Journal of Computer-Aided Molecular Design , vol.22 , pp. 201-212
    • Jain, A.N.1
  • 23
    • 0019402866 scopus 로고
    • Greenland P. Selection and interpretation of diagnostic tests and procedures
    • Griner PF Mayewski RJ Mushlin AI Greenland P. Selection and interpretation of diagnostic tests and procedures Annals of Internal Medicine 1981, 94:555-600
    • (1981) Annals of Internal Medicine , vol.94 , pp. 555-600
    • Griner, P.F.1    Mayewski, R.J.2    Mushlin, A.I.3
  • 24
    • 0018079655 scopus 로고
    • Basic principles of ROC analysis
    • 10.1016/S0001-2998(78)80014-2 112681
    • Metz CE Basic principles of ROC analysis Seminars in Nuclear Medicine 1978, 8:283-298 10.1016/S0001-2998(78)80014-2 112681
    • (1978) Seminars in Nuclear Medicine , vol.8 , pp. 283-298
    • Metz, C.E.1
  • 25
    • 0027457620 scopus 로고
    • Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine
    • 8472349
    • Zweig MH Campbell G Receiver-operating characteristic (ROC) plots: A fundamental evaluation tool in clinical medicine Clinical Chemistry 1993, 39:561-577 8472349
    • (1993) Clinical Chemistry , vol.39 , pp. 561-577
    • Zweig, M.H.1    Campbell, G.2
  • 26
    • 0020083498 scopus 로고
    • The meaning and use of the area under a receiver operating characteristic (ROC) curve
    • 7063747
    • Hanley JA McNeil BJ The meaning and use of the area under a receiver operating characteristic (ROC) curve Radiology 1982, 143:29-36 7063747
    • (1982) Radiology , vol.143 , pp. 29-36
    • Hanley, J.A.1    McNeil, B.J.2
  • 27
    • 0020524559 scopus 로고
    • A method of comparing the areas under receiver operating characteristic curves derived from the same cases
    • 6878708
    • Hanley JA McNeil BJ A method of comparing the areas under receiver operating characteristic curves derived from the same cases Radiology 1983, 148:839-843 6878708
    • (1983) Radiology , vol.148 , pp. 839-843
    • Hanley, J.A.1    McNeil, B.J.2
  • 28
    • 0000924369 scopus 로고    scopus 로고
    • A distribution-free procedure for comparing receiver operating characteristic curves from a paired experiment
    • 10.1093/biomet/83.4.835
    • Venkatraman ES Begg CB A distribution-free procedure for comparing receiver operating characteristic curves from a paired experiment Biometrika 1996, 83:835-848 10.1093/biomet/83.4.835
    • (1996) Biometrika , vol.83 , pp. 835-848
    • Venkatraman, E.S.1    Begg, C.B.2
  • 29
    • 0033635739 scopus 로고    scopus 로고
    • A permutation test to compare receiver operating characteristic curves
    • 10.1111/j.0006-341X.2000.01134.x 11129471
    • Venkatraman ES A permutation test to compare receiver operating characteristic curves Biometrics 2000, 56:1134-8 10.1111/ j.0006-341X.2000.01134.x 11129471
    • (2000) Biometrics , vol.56 , pp. 1134-1138
    • Venkatraman, E.S.1
  • 30
    • 0023710206 scopus 로고    scopus 로고
    • Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach
    • 10.2307/2531595
    • DeLong ER DeLong DM Clarke-Pearson DL Comparing the areas under two or more correlated receiver operating characteristic curves: A nonparametric approach Biometrics 1998, 44:837-845 10.2307/2531595
    • (1998) Biometrics , vol.44 , pp. 837-845
    • DeLong, E.R.1    DeLong, D.M.2    Clarke-Pearson, D.L.3
  • 31
    • 49549139345 scopus 로고
    • The area above the ordinal dominance graph and the area below the receiver operating characteristic curve
    • 10.1016/0022-2496(75)90001-2
    • Bamber D The area above the ordinal dominance graph and the area below the receiver operating characteristic curve Journal of Mathematical Psychology 1975, 12:387-415 10.1016/0022-2496(75)90001-2
    • (1975) Journal of Mathematical Psychology , vol.12 , pp. 387-415
    • Bamber, D.1
  • 32
    • 0029784933 scopus 로고    scopus 로고
    • A simple method for comparing correlated ROC curves using incomplete data
    • Zhou XH Gatsonis CA A simple method for comparing correlated ROC curves using incomplete data Statistics in Medicine 1998, 15:11687-1693
    • (1998) Statistics in Medicine , vol.15 , pp. 11687-11693
    • Zhou, X.H.1    Gatsonis, C.A.2


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