메뉴 건너뛰기




Volumn 2, Issue C, 2006, Pages 297-323

Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding - Consensus and Caveats

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77956760347     PISSN: 15741400     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S1574-1400(06)02016-0     Document Type: Review
Times cited : (9)

References (50)
  • 2
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening accuracy
    • Kellenberger E., Rodrigo J., Muller P., and Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57 (2004) 225-242
    • (2004) Proteins , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 3
    • 0038185582 scopus 로고    scopus 로고
    • Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
    • Schulz-Gasch T., and Stahl M. Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools. J. Mol. Model (Online). 9 (2003) 47-57
    • (2003) J. Mol. Model (Online). , vol.9 , pp. 47-57
    • Schulz-Gasch, T.1    Stahl, M.2
  • 4
    • 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., and Davies J.W. Finding more needles in the haystack: A simple and efficient method for improving high-throughput docking results. J. Med. Chem. 47 (2004) 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
  • 5
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • Perola E., Walters W.P., and Charifson P.S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56 (2004) 235-249
    • (2004) Proteins , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 6
    • 1642378145 scopus 로고    scopus 로고
    • Virtual screening for kinase targets
    • Muegge I., and Enyedy I.J. Virtual screening for kinase targets. Curr. Med. Chem. 11 (2004) 693-707
    • (2004) Curr. Med. Chem. , vol.11 , pp. 693-707
    • Muegge, I.1    Enyedy, I.J.2
  • 8
    • 11144255694 scopus 로고    scopus 로고
    • Evaluation of library ranking efficacy in virtual screening
    • Kontoyianni M., Sokol G.S., and McClellan L.M. Evaluation of library ranking efficacy in virtual screening. J. Comput. Chem. 26 (2005) 11-22
    • (2005) J. Comput. Chem. , vol.26 , pp. 11-22
    • Kontoyianni, M.1    Sokol, G.S.2    McClellan, L.M.3
  • 9
    • 33749260698 scopus 로고    scopus 로고
    • G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head, J. Med. Chem., A critical assessment of docking programs and scoring functions, 2005, ASAP Article, DOI: 10.1021/jm050362n.
    • G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head, J. Med. Chem., A critical assessment of docking programs and scoring functions, 2005, ASAP Article, DOI: 10.1021/jm050362n.
  • 10
    • 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., and Li J. On evaluating molecular-docking methods for pose prediction and enrichment factors. J. Chem. Inf. Model. 46 (2006) 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
  • 12
    • 3242884966 scopus 로고    scopus 로고
    • High-throughput docking as a source of novel drug leads
    • Alvarez J.C. High-throughput docking as a source of novel drug leads. Curr. Opin. Chem. Biol. 8 (2004) 365-370
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 365-370
    • Alvarez, J.C.1
  • 13
  • 14
    • 0035025191 scopus 로고    scopus 로고
    • I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • Ewing T.J.M., Skillman S., and Kuntz A.G. I.D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases,. J. Comput. Aided. Mol. Des. 15 (2001) 411-428
    • (2001) J. Comput. Aided. Mol. Des. , vol.15 , pp. 411-428
    • Ewing, T.J.M.1    Skillman, S.2    Kuntz, A.G.3
  • 15
    • 77956773039 scopus 로고    scopus 로고
    • J. M. Blaney, and J. S. Dixon, 1.0 eds, Metaphorics, LLC, Mission Viejo, CA.
    • J. M. Blaney, and J. S. Dixon, 1.0 eds, Metaphorics, LLC, Mission Viejo, CA.
  • 16
    • 0026780930 scopus 로고
    • A multiple-start Monte Carlo docking method
    • Hart T.N., and Read R.J. A multiple-start Monte Carlo docking method. Proteins 13 (1992) 206-222
    • (1992) Proteins , vol.13 , pp. 206-222
    • Hart, T.N.1    Read, R.J.2
  • 17
    • 0031297617 scopus 로고    scopus 로고
    • Critical evaluation of the research docking program for the CASP2 challenge
    • Hart T.N., Ness S.R., and Read R.J. Critical evaluation of the research docking program for the CASP2 challenge. Proteins Suppl 1 (1997) 205-209
    • (1997) Proteins , vol.SUPPL. 1 , pp. 205-209
    • Hart, T.N.1    Ness, S.R.2    Read, R.J.3
  • 18
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M., Kramer B., Lengauer T., and Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261 (1996) 470-489
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 19
    • 0031181346 scopus 로고    scopus 로고
    • QXP: Powerful, rapid computer algorithms for structure-based drug design
    • McMartin C., and Bohacek R.S. QXP: Powerful, rapid computer algorithms for structure-based drug design. J. Comput. Aided. Mol. Des. 11 (1997) 333-344
    • (1997) J. Comput. Aided. Mol. Des. , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 22
    • 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., and Banks J.L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J. Med. Chem. 47 (2004) 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
  • 23
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G., Willett P., Glen R.C., Leach A.R., and Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267 (1997) 727-748
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 24
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R.T., and Kuznetsov M.R. ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15 (1994) 488-506
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.T.1    Kuznetsov, M.R.2
  • 25
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam C.M., Jiang X., Oldfield T., and Waldman M. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model. 21 (2003) 289-307
    • (2003) J. Mol. Graph. Model. , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 26
    • 77956726569 scopus 로고    scopus 로고
    • Chemical Computing Group, Montreal, QC, Canada
    • Chemical Computing Group, Montreal, QC, Canada.
  • 28
    • 0037434582 scopus 로고    scopus 로고
    • Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
    • Jain A.N. Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem. 46 (2003) 499-511
    • (2003) J. Med. Chem. , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 29
    • 0027379219 scopus 로고
    • Orientational sampling and rigid-body minimization in molecular docking
    • Meng E.C., Gschwend D.A., Blaney J.M., and Kuntz I.D. Orientational sampling and rigid-body minimization in molecular docking. Proteins 17 (1993) 266-278
    • (1993) Proteins , vol.17 , pp. 266-278
    • Meng, E.C.1    Gschwend, D.A.2    Blaney, J.M.3    Kuntz, I.D.4
  • 30
    • 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
    • Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., and Mee R.P. 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
  • 31
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • Rarey M., Wefing S., and Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J. Comput. Aided. Mol. Des. 10 (1996) 41-54
    • (1996) J. Comput. Aided. Mol. Des. , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 32
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • Wang R., Lai L., and Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput. Aided. Mol. Des. 16 (2002) 11-26
    • (2002) J. Comput. Aided. Mol. Des. , vol.16 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 34
    • 0033566211 scopus 로고    scopus 로고
    • Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
    • Muegge I., Martin Y.C., Hajduk P.J., and Fesik S.W. Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J. Med. Chem. 42 (1999) 2498-2503
    • (1999) J. Med. Chem. , vol.42 , pp. 2498-2503
    • Muegge, I.1    Martin, Y.C.2    Hajduk, P.J.3    Fesik, S.W.4
  • 35
    • 10044294023 scopus 로고    scopus 로고
    • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
    • Wang R., Lu Y., Fang X., and Wang S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 44 (2004) 2114-2125
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 2114-2125
    • Wang, R.1    Lu, Y.2    Fang, X.3    Wang, S.4
  • 36
    • 5344237409 scopus 로고    scopus 로고
    • Assessing the impact of high-performance computing on the drug discovery and development process
    • Scott R.K. Assessing the impact of high-performance computing on the drug discovery and development process. DDT, Biosilico 2 (2004) 175-179
    • (2004) DDT, Biosilico , vol.2 , pp. 175-179
    • Scott, R.K.1
  • 37
    • 0038460858 scopus 로고    scopus 로고
    • Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
    • McGovern S.L., and Shoichet B.K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes. J. Med. Chem. 46 (2003) 2895-2907
    • (2003) J. Med. Chem. , vol.46 , pp. 2895-2907
    • McGovern, S.L.1    Shoichet, B.K.2
  • 38
    • 33244475355 scopus 로고    scopus 로고
    • Screening drug-like compounds by docking to homology models: A systematic study
    • Kairys V., Fernandes M.X., and Gilson M.K. Screening drug-like compounds by docking to homology models: A systematic study. J. Chem. Inf. Model. 46 (2006) 365-379
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 365-379
    • Kairys, V.1    Fernandes, M.X.2    Gilson, M.K.3
  • 41
    • 0037208312 scopus 로고    scopus 로고
    • Consideration of molecular weight during compound selection in virtual target-based database screening
    • Pan Y., Huang N., Cho S., and MacKerell Jr. A.D. Consideration of molecular weight during compound selection in virtual target-based database screening. J. Chem. Inf. Comput. Sci. 43 (2003) 267-272
    • (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
  • 42
    • 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., and 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. 48 (2005) 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
  • 43
    • 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., and Kearsley S.K. Protocols for bridging the peptide to nonpeptide gap in topological similarity searches. J. Chem. Inf. Comput. Sci. 41 (2001) 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
  • 44
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar D.K., Verkhivker G.M., Rejto P.A., Sherman C.J., Fogel D.B., Fogel L.J., and Freer S.T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 2 (1995) 317-324
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 46
    • 3342933156 scopus 로고    scopus 로고
    • Target-biased scoring approaches and expert systems in structure-based virtual screening
    • Jansen J.M., and Martin E.J. Target-biased scoring approaches and expert systems in structure-based virtual screening. Curr. Opin. Chem. Biol. 8 (2004) 359-364
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 359-364
    • Jansen, J.M.1    Martin, E.J.2
  • 47
    • 0346996357 scopus 로고    scopus 로고
    • Improving structure-based virtual screening by multivariate analysis of scoring data
    • Jacobsson M., Liden P., Stjernschantz E., Bostrom H., and Norinder U. Improving structure-based virtual screening by multivariate analysis of scoring data. J. Med. Chem. 46 (2003) 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
  • 48
    • 27444445346 scopus 로고    scopus 로고
    • PostDOCK: A structural, empirical approach to scoring protein ligand complexes
    • Springer C., Adalsteinsson H., Young M.M., Kegelmeyer P.W., and Roe D.C. PostDOCK: A structural, empirical approach to scoring protein ligand complexes. J. Med. Chem. 48 (2005) 6821-6831
    • (2005) J. Med. Chem. , vol.48 , pp. 6821-6831
    • Springer, C.1    Adalsteinsson, H.2    Young, M.M.3    Kegelmeyer, P.W.4    Roe, D.C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.