메뉴 건너뛰기




Volumn 47, Issue 4, 2007, Pages 1504-1519

Comparison of topological, shape, and docking methods in virtual screening

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BENCHMARKING; DATABASE SYSTEMS; LIGANDS; MOLECULAR STRUCTURE;

EID: 34547673017     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700052x     Document Type: Article
Times cited : (382)

References (52)
  • 2
    • 33244483907 scopus 로고    scopus 로고
    • On evaluating molecular-docking methods for pose prediction and enrichment factors
    • Chen, H.; Lyne, P. D.; Giordanetto, F.; Lovell, T.; Li, J. On evaluating molecular-docking methods for pose prediction and enrichment factors. J. Chem. Inf. Model. 2006, 46, 401-415.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 401-415
    • Chen, H.1    Lyne, P.D.2    Giordanetto, F.3    Lovell, T.4    Li, J.5
  • 3
    • 2442716437 scopus 로고    scopus 로고
    • Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results
    • Klon, A. E.; Glick, M.; Thoma, M.; Acklin, P.; Davies, J. W. Finding More Needles in the Haystack: A Simple and Efficient Method for Improving High-Throughput Docking Results. J. Med. Chem. 2004, 47, 2743-2749.
    • (2004) J. Med. Chem , vol.47 , pp. 2743-2749
    • Klon, A.E.1    Glick, M.2    Thoma, M.3    Acklin, P.4    Davies, J.W.5
  • 4
    • 3042806401 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, 56, 235-249.
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 5
    • 1642378145 scopus 로고    scopus 로고
    • Virtual screening for kinase targets
    • Muegge, I.; Enyedy, I. J. Virtual screening for kinase targets. Curr. Med. Chem. 2004, 11, 693-707.
    • (2004) Curr. Med. Chem , vol.11 , pp. 693-707
    • Muegge, I.1    Enyedy, I.J.2
  • 7
    • 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
  • 8
    • 33749260698 scopus 로고    scopus 로고
    • Warren, G. L.; Andrews, C. W.; Capelli, A.-M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2005, 49, 5912-5931.
    • Warren, G. L.; Andrews, C. W.; Capelli, A.-M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2005, 49, 5912-5931.
  • 9
    • 85057214100 scopus 로고    scopus 로고
    • Shoichet, N, Alvarez, J, Eds, CRC Press
    • Virtual Screening in Drug Discovery; Shoichet, N., Alvarez, J., Eds.; CRC Press: 2005.
    • (2005) Virtual Screening in Drug Discovery
  • 10
    • 77956760347 scopus 로고    scopus 로고
    • Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding - Consensus and Caveats
    • Spellmeyer, D. C, Ed, Elsevier: Amsterdam
    • Cornell, W. D. Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding - Consensus and Caveats. In Annual Reports in Computational Chemistry (ARCC) Volume 2; Spellmeyer, D. C., Ed.; Elsevier: Amsterdam, 2006.
    • (2006) Annual Reports in Computational Chemistry (ARCC) , vol.2
    • Cornell, W.D.1
  • 11
    • 84944662266 scopus 로고
    • A new series of anticonvulsant drugs tested by experiments on animals
    • Merritt, H. H.; Putnam. T. J. A new series of anticonvulsant drugs tested by experiments on animals. Arch. Neur. Psych. 1938, 39, 1003-1015.
    • (1938) Arch. Neur. Psych , vol.39 , pp. 1003-1015
    • Merritt, H.H.1    Putnam, T.J.2
  • 12
    • 34547712142 scopus 로고    scopus 로고
    • Abstracts of Papers, 231st ACS National Meeting, Atlanta, GA, United States, March 26-30
    • van Drie, J. Pharmacophore-based virtual screening. Abstracts of Papers, 231st ACS National Meeting, Atlanta, GA, United States, March 26-30, 2006.
    • (2006) Pharmacophore-based virtual screening
    • van Drie, J.1
  • 13
    • 0028412035 scopus 로고
    • FLOG: A system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure
    • Miller, M. D.; Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P. FLOG: a system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 153-174.
    • (1994) J. Comput.-Aided Mol. Des , vol.8 , pp. 153-174
    • Miller, M.D.1    Kearsley, S.K.2    Underwood, D.J.3    Sheridan, R.P.4
  • 14
    • 0033529045 scopus 로고    scopus 로고
    • A program for rapidly producing pharmacophorically relevant molecular superpositions
    • Miller, M. D.; Sheridan, R. P.; Kearsley, S. L. SQ: A program for rapidly producing pharmacophorically relevant molecular superpositions. J. Med. Chem. 1999, 42, 1505-1514.
    • (1999) J. Med. Chem , vol.42 , pp. 1505-1514
    • Miller, M.D.1    Sheridan, R.P.2    Kearsley, S.L.S.3
  • 15
    • 0035324941 scopus 로고    scopus 로고
    • Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations
    • Feuston, B. P.; Miller, M. D.; Culberson, J. C.; Nachbar, R. B.; Kearsley, S. K. Comparison of knowledge-based and distance geometry approaches for generation of molecular conformations. J. Chem. Inf. Comput. Sci. 2001, 41, 754-763.
    • (2001) J. Chem. Inf. Comput. Sci , vol.41 , pp. 754-763
    • Feuston, B.P.1    Miller, M.D.2    Culberson, J.C.3    Nachbar, R.B.4    Kearsley, S.K.5
  • 17
    • 0026676167 scopus 로고
    • Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm
    • Kuszewski, J.; Nilges, M.; Brunger, A. T. Sampling and efficiency of metric matrix distance geometry: A novel partial metrization algorithm. J. Biomol. NMR 1992, 2, 33-56.
    • (1992) J. Biomol. NMR , vol.2 , pp. 33-56
    • Kuszewski, J.1    Nilges, M.2    Brunger, A.T.3
  • 19
    • 1642310340 scopus 로고    scopus 로고
    • 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.
    • 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.
  • 20
    • 12144289984 scopus 로고    scopus 로고
    • Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
    • Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
  • 23
    • 34547694898 scopus 로고    scopus 로고
    • Daylight Chemical Information Systems, Inc. Version 4.82; 120 Vantis, Suite 550, Aliso Viejo, CA 92656, 2003
    • Daylight Chemical Information Systems, Inc. Version 4.82; 120 Vantis, Suite 550, Aliso Viejo, CA 92656, 2003.
  • 24
    • 34547710570 scopus 로고    scopus 로고
    • MDL Drug Data Report, version 2005.1; licensed by Molecular Design Ltd, San Leandro, CA, 2005
    • MDL Drug Data Report, version 2005.1; licensed by Molecular Design Ltd., San Leandro, CA, 2005.
  • 25
    • 33244475355 scopus 로고    scopus 로고
    • Screening drug-like compounds by docking to homology models: A Systematic Study
    • Kairys, V.; Fernandes, M. X.; Gilson, M. K. Screening drug-like compounds by docking to homology models: A Systematic Study. J. Chem. Inf. Model. 2006, 46, 365-379.
    • (2006) J. Chem. Inf. Model , vol.46 , pp. 365-379
    • Kairys, V.1    Fernandes, M.X.2    Gilson, M.K.3
  • 26
    • 0032671931 scopus 로고    scopus 로고
    • Unsupervised data base clustering based on Daylight's fingerprint and Tanimoto similarity: A fast and automated way to cluster small and large data sets
    • Butina, D. Unsupervised data base clustering based on Daylight's fingerprint and Tanimoto similarity: a fast and automated way to cluster small and large data sets. J. Chem. Inf. Comput. Sci. 1999, 39, 747-750.
    • (1999) J. Chem. Inf. Comput. Sci , vol.39 , pp. 747-750
    • Butina, D.1
  • 27
    • 33845379303 scopus 로고
    • Atom pairs as molecular features in structure-activity studies: Definition and applications
    • Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: definition and applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
    • (1985) J. Chem. Inf. Comput. Sci , vol.25 , pp. 64-73
    • Carhart, R.E.1    Smith, D.H.2    Venkataraghavan, R.3
  • 28
    • 34547721379 scopus 로고    scopus 로고
    • personal communication
    • Bradshaw, J., personal communication.
    • Bradshaw, J.1
  • 29
    • 0028522982 scopus 로고    scopus 로고
    • Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P.; Miller, M. D. Flexibases: a way to enhance the use of molecular docking methods. J. Comput.-Aided Mol. Des. 1994, 8, 565-582.
    • Kearsley, S. K.; Underwood, D. J.; Sheridan, R. P.; Miller, M. D. Flexibases: a way to enhance the use of molecular docking methods. J. Comput.-Aided Mol. Des. 1994, 8, 565-582.
  • 31
    • 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: Struct., Funct., Bioinf. 2004, 57, 225-242.
    • (2004) Proteins: Struct., Funct., Bioinf , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 32
    • 0037208312 scopus 로고    scopus 로고
    • Consideration of molecular weight during compound selection in virtual target-based database screening
    • Pan, Y.; Huang, N.; Cho, S.; MacKerell, A. D., Jr. Consideration of molecular weight during compound selection in virtual target-based database screening. J. Chem. Inf. Comput. Sci. 2003, 43, 267-72.
    • (2003) J. Chem. Inf. Comput. Sci , vol.43 , pp. 267-272
    • Pan, Y.1    Huang, N.2    Cho, S.3    MacKerell Jr., A.D.4
  • 33
    • 0346731233 scopus 로고    scopus 로고
    • Multiple active site corrections for docking and virtual screening
    • Vigers, G. P. A.; Rizzi, J. P. Multiple active site corrections for docking and virtual screening. J. Med. Chem. 2004, 47, 80-89.
    • (2004) J. Med. Chem , vol.47 , pp. 80-89
    • Vigers, G.P.A.1    Rizzi, J.P.2
  • 34
    • 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
    • Triballeau, N.; Acher, F.; Brabet, I.; Pin, J.-P.; Bertrand, H.-O. Virtual screening workflow development guided by the 'receiver operating characteristic' curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J. Med. Chem. 2005, 48, 2534-2547.
    • (2005) J. Med. Chem , vol.48 , pp. 2534-2547
    • Triballeau, N.1    Acher, F.2    Brabet, I.3    Pin, J.-P.4    Bertrand, H.-O.5
  • 35
    • 0035438401 scopus 로고    scopus 로고
    • Protocols for bridging the peptide to nonpeptide gap in topological similarity searches
    • Sheridan, R. P.; Singh, S. B.; Fluder, E. M.; Kearsley, S. K. Protocols for bridging the peptide to nonpeptide gap in topological similarity searches. J. Chem. Inf. Comput. Sci. 2001, 41, 1395-1406.
    • (2001) J. Chem. Inf. Comput. Sci , vol.41 , pp. 1395-1406
    • Sheridan, R.P.1    Singh, S.B.2    Fluder, E.M.3    Kearsley, S.K.4
  • 36
    • 34247272948 scopus 로고    scopus 로고
    • Evaluating Virtual Screening Methods: Good and Bad Metrics for the Early Recognition Problem
    • Truchon, J.-F.; Bayly, C. I., Evaluating Virtual Screening Methods: Good and Bad Metrics for the Early Recognition Problem. J. Chem. Inf. Model. 2007, 47, 488-508.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 488-508
    • Truchon, J.-F.1    Bayly, C.I.2
  • 37
    • 0038185582 scopus 로고    scopus 로고
    • Schulz-Gasch, T.; Stahl, M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J. Mol. Model. (Online) 2003, 9, 47-57. Enrichment values were extracted from the histograms depicted in the manuscript.
    • Schulz-Gasch, T.; Stahl, M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J. Mol. Model. (Online) 2003, 9, 47-57. Enrichment values were extracted from the histograms depicted in the manuscript.
  • 38
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity? J. Med. Chem. 2002, 45, 4350-4358.
    • (2002) J. Med. Chem , vol.45 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 39
    • 1042265247 scopus 로고    scopus 로고
    • Approaches to measure chemical similarity-a review
    • Nikolova, N.; Jaworska, J. Approaches to measure chemical similarity-a review. QSAR Comb. Sci. 2003, 22, 1006-1026.
    • (2003) QSAR Comb. Sci , vol.22 , pp. 1006-1026
    • Nikolova, N.1    Jaworska, J.2
  • 40
    • 0036740917 scopus 로고    scopus 로고
    • Why do we need so many chemical similarity methods
    • Sheridan, R. P.; Kearsley, S. K. Why do we need so many chemical similarity methods. Drug Discovery Today 2002, 7, 903-911.
    • (2002) Drug Discovery Today , vol.7 , pp. 903-911
    • Sheridan, R.P.1    Kearsley, S.K.2
  • 41
    • 33644862638 scopus 로고    scopus 로고
    • Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
    • Zhang, Q.; Muegge, I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring. J. Med. Chem. 2006, 49, 1536-1548.
    • (2006) J. Med. Chem , vol.49 , pp. 1536-1548
    • Zhang, Q.1    Muegge, I.2
  • 42
    • 20844436604 scopus 로고    scopus 로고
    • Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
    • Good, A. C.; Hermsmeier, M. A.; Hindle, S. A. Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments. J. Comput.-Aided Mol. Des. 2004, 18, 529-536.
    • (2004) J. Comput.-Aided Mol. Des , vol.18 , pp. 529-536
    • Good, A.C.1    Hermsmeier, M.A.2    Hindle, S.A.3
  • 43
    • 28944437859 scopus 로고    scopus 로고
    • Considerations in compound database preparation - hidden impact on virtual screening results
    • Knox, A. J. S.; Meegan, M. J.; Carta, G.; Lloyd, D. G. Considerations in compound database preparation - hidden impact on virtual screening results. J. Chem. Inf. Comput. Sci. 2005, 45, 1908-1919.
    • (2005) J. Chem. Inf. Comput. Sci , vol.45 , pp. 1908-1919
    • Knox, A.J.S.1    Meegan, M.J.2    Carta, G.3    Lloyd, D.G.4
  • 44
    • 0032708785 scopus 로고    scopus 로고
    • Efficacy and selectivity in flexible database docking
    • Knegtel, R. M. A.; Wagener, M. Efficacy and selectivity in flexible database docking. Proteins 1999, 37, 334-345.
    • (1999) Proteins , vol.37 , pp. 334-345
    • Knegtel, R.M.A.1    Wagener, M.2
  • 46
    • 33846212271 scopus 로고    scopus 로고
    • Comparison of Shape-Matching and Docking as Virtual Screening Tools
    • Hawkins, P. C. D.; Skillman, A. G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools. J. Med. Chem. 2007, 50, 74-82.
    • (2007) J. Med. Chem , vol.50 , pp. 74-82
    • Hawkins, P.C.D.1    Skillman, A.G.2    Nicholls, A.3
  • 47
    • 34247260419 scopus 로고    scopus 로고
    • Comments on the Article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors
    • Perola, E.; Walters, W. P.; Charifson, P. Comments on the Article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors". J. Chem. Inf. Model. 2007, 47, 251-253.
    • (2007) J. Chem. Inf. Model , vol.47 , pp. 251-253
    • Perola, E.1    Walters, W.P.2    Charifson, P.3
  • 48
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- and three-dimensional structures
    • Willett, P. Searching techniques for databases of two- and three-dimensional structures. J. Med. Chem. 2005, 48, 4183-4199.
    • (2005) J. Med. Chem , vol.48 , pp. 4183-4199
    • Willett, P.1
  • 49
    • 33749242759 scopus 로고    scopus 로고
    • Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
    • Tirado-Rives, J.; Jorgensen, W. L. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J. Med. Chem. 2006, 49, 5880-5894.
    • (2006) J. Med. Chem , vol.49 , pp. 5880-5894
    • Tirado-Rives, J.1    Jorgensen, W.L.2
  • 50
    • 33749245117 scopus 로고    scopus 로고
    • Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps
    • Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps. J. Med. Chem. 2006, 49, 5851-5855.
    • (2006) J. Med. Chem , vol.49 , pp. 5851-5855
    • Leach, A.R.1    Shoichet, B.K.2    Peishoff, C.E.3
  • 52
    • 33750991346 scopus 로고    scopus 로고
    • Benchmarking Sets for Molecular Docking
    • Huang, N.; Shoichet, B. K.; 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    Shoichet, B.K.2    Irwin, J.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.