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Volumn 46, Issue 1, 2006, Pages 401-415

On evaluating molecular-docking methods for pose prediction and enrichment factors

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; DIGITAL LIBRARIES; DRUG THERAPY; FUNCTION EVALUATION; PROTEINS; VIRTUAL REALITY;

EID: 33244483907     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci0503255     Document Type: Conference Paper
Times cited : (221)

References (57)
  • 1
    • 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 2004, 2, 175-179.
    • (2004) DDT: Biosilico , vol.2 , pp. 175-179
    • Scott, R.K.1
  • 3
    • 0033915982 scopus 로고    scopus 로고
    • Recent advances in structure-based rational drug design
    • (b) Gane, P. J.; Dean, P. M. Recent advances in structure-based rational drug design. Curr. Opin. Struct. Biol. 2000, 10, 401-404.
    • (2000) Curr. Opin. Struct. Biol. , vol.10 , pp. 401-404
    • Gane, P.J.1    Dean, P.M.2
  • 5
    • 0035416126 scopus 로고    scopus 로고
    • High-throughput docking for lead generation
    • (b) Abagyan, R.; Totrov, M. High-throughput docking for lead generation. Curr. Opin. Chem. Biol. 2001, 5, 375-382.
    • (2001) Curr. Opin. Chem. Biol. , vol.5 , pp. 375-382
    • Abagyan, R.1    Totrov, M.2
  • 7
    • 0036835460 scopus 로고    scopus 로고
    • Integration of virtual and high-throughput screening
    • (a) Bajorath, J. Integration of virtual and high-throughput screening. Na. Rev. Drug Discovery 2002, 1, 882-894.
    • (2002) Na. Rev. Drug Discovery , vol.1 , pp. 882-894
    • Bajorath, J.1
  • 8
    • 0037107887 scopus 로고    scopus 로고
    • Structure based virtual screening: An overview
    • (b) Lyne, P. D. Structure based virtual screening: an overview. Drug Discovery Today 2002, 7, 1047-1055.
    • (2002) Drug Discovery Today , vol.7 , pp. 1047-1055
    • Lyne, P.D.1
  • 9
    • 0034581968 scopus 로고    scopus 로고
    • High-throughput and virtual screening: Core lead discovery technologies move towards integration
    • (c) Good, A. C.; Krystek, S. R.; Mason, J. S. High-throughput and virtual screening: core lead discovery technologies move towards integration. Drug Discovery Today 2002, 5, S61-S69.
    • (2002) Drug Discovery Today , vol.5
    • Good, A.C.1    Krystek, S.R.2    Mason, J.S.3
  • 10
    • 0036007208 scopus 로고    scopus 로고
    • Virtual screening and fast automated docking methods
    • Schneider, G.; Bohn, H.-J. Virtual screening and fast automated docking methods. Drug Discovery Today 2002, 7, 64-70.
    • (2002) Drug Discovery Today , vol.7 , pp. 64-70
    • Schneider, G.1    Bohn, H.-J.2
  • 11
    • 33244463667 scopus 로고    scopus 로고
    • The emergence of in silico methodologies
    • in press
    • (e) Li, J.; Lovell, T. The emergence of in silico methodologies. World Pharm. Frontiers 2005, in press.
    • (2005) World Pharm. Frontiers
    • Li, J.1    Lovell, T.2
  • 12
    • 0001139413 scopus 로고    scopus 로고
    • Automated flexible ligand docking method and its application for database search
    • Makino, S.; Kuntz, I. D. Automated flexible ligand docking method and its application for database search. J. Comput. Chem. 1997, 18, 1812-1825.
    • (1997) J. Comput. Chem. , vol.18 , pp. 1812-1825
    • Makino, S.1    Kuntz, I.D.2
  • 13
    • 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, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 14
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, R.; Glen, R.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, R.2    Glen, R.3    Leach, A.R.4    Taylor, R.5
  • 15
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.3    Huey, R.4    Hart, W.E.5    Belew, R.K.6    Olson, A.J.7
  • 17
    • 0031181346 scopus 로고    scopus 로고
    • QXP: Powerful, rapid computer algorithms for structure-based drug design
    • McMartin, C.; Bohacek, R. S. QXP: Powerful, rapid computer algorithms for structure-based drug design. J. Comput.-Aided Mol. Des. 1997, 11, 333-344.
    • (1997) J. Comput.-aided Mol. Des. , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 18
    • 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.; Totrov, M.; Kuznetsov, R. ICM - A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 1994, 15, 488-506.
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, R.3
  • 21
    • 3042806401 scopus 로고    scopus 로고
    • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
    • (c) Perola, E.; Walters, W. P.; Charifson, P. S. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins: Struct., Funct., Bioinf. 2004, 56, 235-249.
    • (2004) Proteins: Struct., Funct., Bioinf. , vol.56 , pp. 235-249
    • Perola, E.1    Walters, W.P.2    Charifson, P.S.3
  • 22
    • 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
  • 23
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • (e) Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of Docking Performance: Comparative Data on Docking Algorithms. J. Med. Chem. 2004, 47, 558-565.
    • (2004) J. Med. Chem. , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 24
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • (f) 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
  • 25
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening accuracy
    • (g) 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
  • 31
    • 0037666888 scopus 로고    scopus 로고
    • Implications for protein flexibility for drug discovery
    • Teague, S. J. Implications for protein flexibility for drug discovery. Nature Rev. Drug Discovery 2003, 2, 527-541.
    • (2003) Nature Rev. Drug Discovery , vol.2 , pp. 527-541
    • Teague, S.J.1
  • 32
    • 84888781563 scopus 로고    scopus 로고
    • note
    • The PDB identification codes of the publicly available proteins studied in this work along with their resolutions in Å are given: 1 aaq 2.50, 1abe 1.70, 1abf 1.90, 1acm 2.80, 1acl 2.80, 1acj 2.80, 1add 2.40, 1aha 2.20, 1apu 1.80, 1apt 1.80, 1aqw 1.80, 1aqx 2.00, 1atl 1.80, 1azm 2.00, 1b8y 2.00, 1baf 2.90, 1bbp 2.00, 1bcu 2.00, 1bhx 2.30, 1bji 2.00, 1cbs 1.80, 1cbx 2.00, 1cil 1.60, 1ciz 1.64, 1com 2.20, 1coy 1.80, 1cps 2.25, 1ctt 2.20, 1dbb 2.70, 1dbj 2.70, 1did 2.50, 1die 2.50, 1dmp 2.00, 1dog 2.40, 1dth 2.00, 1dwb 3.16, 1dwd 3.00, leap 2.50, 1ebg 2.10, 1eed 2.00, 1ela 1.80, 1elb 2.10, 1elc 1.75, 1epb 2.20, 1epo 2.00, 1ere 3.10, 1err 2.60, 1etr 2.20, 1ett 2.50, 1fax 3.00, 1fkg 2.00, 1fki 2.20, 1frp 2.00, 1glp 1.90, 1glq 1.80, 1hck 1.90, 1hdc 2.20, 1hfc 1.56, 1hfs 1.70, 1hpv 1.90, 1hri 3.00, 1hsl 1.89, 1htf 2.20, 1hvr 1.80, 1hyt 1.70, 1icn 1.74, 1igj 2.50, 1imb 2.20, live 2.40, 1jao 2.40, 1lah 2.06, 1lcp 1.65, 1ldm 2.10, 1lic 1.60, 1lmo 1.80, 1lst 1.80, 1mcr 2.70, 1mdr 2.10, 1mmb 2.10, 1mmq 1.90, 1mnc 2.10, 1mrg 1.80, 1mrk 1.60, 1mtw 1.90, 1mup 2.40, 1nco 1.80, 1nsd 1.80, 1ohj 2.50, 1okl 2.10, 1okm 2.20, 1pbd 2.30, 1phf 1.60, 1ppc 1.80, 1pph 1.90, 1poc 2.00, 1qbt 2.10, 1qbu 1.80, 1rbp 2.00, 1rne 2.40, 1rob 1.60, 1sln 2.27, 1snc 1.65, 1srj 1.80, 1stp 2.60, 1tka 2.70, 1tng 1.80, 1tnh 1.80, 1tnl 1.90, 1tph 1.80, 1tpp 1.40. 1uag 1.95, 1ukz 1.90, 1ulb 2.75, 1usn 1.80, 1uvs 2.80, 1uvt 2.50, 1wap 1.80, 1web 1.50, 1wec 1.50, 1wed 1.50, 1xid 1.70, 1xie 1.70, 1xug 1.50, 1ydr 2.20, 1yds 2.20, 1ydt 2.30, 2ada 2.40, 2cgr 2.20, 2cht 2.20, 2cmd 1.87, 2cpp 1.63, 2ctc 1.40, 2dbl 2.90, 2gbp 1.90, 2h4n 1.90, 2ifb 2.00, 2phh 2.70, 2sim 1.60, 2tmn 1.60, 2tsc 1.97, 2usn 2.20, 2ypi 2.50, 3aah 2.40, 3cla 1.75, 3erd 2.03, 3ert 1.90, 3hvt 2.90, 3ptb 1.70, 3tpi 1.90, 4cts 2.90, 4dfr 1.70, 4fab 2.70, 4phv 2.10, 4tim 2.40, 4tpi 2.20, 5abp 1.80, 5tim 1.83, 5tln 2.30, 6abp 1.67, 6cpa 2.00, 6rnt 1.80, 7tim 1.90, 8ate 2.50, 8gch 1.60.
  • 33
    • 0003497170 scopus 로고    scopus 로고
    • Tripos Inc.: St. Louis, MO
    • Sybyl, version 6.5; Tripos Inc.: St. Louis, MO.
    • Sybyl, Version 6.5
  • 34
    • 33244487726 scopus 로고    scopus 로고
    • Schrödinger LLC: New York
    • Glide, version 3.5; Schrödinger LLC: New York, 2005.
    • (2005) Glide, Version 3.5
  • 35
    • 33244485199 scopus 로고    scopus 로고
    • Molsoft LLC: San Diego, CA
    • ICM, version 3.2.01a; Molsoft LLC: San Diego, CA, 2004.
    • (2004) ICM, Version 3.2.01a
  • 36
    • 31444452744 scopus 로고
    • Automatic generation of 3D atomic coordinates for organic molecules
    • Gasteiger, J.; Rudolph, C.; Sadowski, J. Automatic generation of 3D atomic coordinates for organic molecules. Tetrahedron Comput. Methodol. 1990, 3, 537-5547.
    • (1990) Tetrahedron Comput. Methodol. , vol.3 , pp. 537-5547
    • Gasteiger, J.1    Rudolph, C.2    Sadowski, J.3
  • 38
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 39
    • 0037571112 scopus 로고
    • Merck molecular force field: 1. Basis, form, scope, parametrization, and performance of MMFF94
    • Halgren, T. A. Merck molecular force field: 1. Basis, form, scope, parametrization, and performance of MMFF94. J. Comput. Chem. 1995, 17, 490-519.
    • (1995) J. Comput. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 40
    • 84888773232 scopus 로고    scopus 로고
    • Openeye Scientific Software LLC: Santa Fe, New Mexico
    • ROCS, version 2.0; Openeye Scientific Software LLC: Santa Fe, New Mexico.
    • ROCS, Version 2.0
  • 41
    • 84888797013 scopus 로고    scopus 로고
    • MDL Information Systems, Inc.: San Leandro, CA
    • ISIS/Base, version 2.3; MDL Information Systems, Inc.: San Leandro, CA.
    • ISIS/Base, Version 2.3
  • 42
    • 84986467005 scopus 로고
    • Conformational analysis of flexible ligands in macromolecular receptor sites
    • Leach, A. R.; Kuntz, I. D. Conformational analysis of flexible ligands in macromolecular receptor sites, J. Comput. Chem. 1992, 13, 730-748.
    • (1992) J. Comput. Chem. , vol.13 , pp. 730-748
    • Leach, A.R.1    Kuntz, I.D.2
  • 44
    • 0027658106 scopus 로고
    • A novel computational tool for automated structure-based drug design
    • Böhm, H. J. A novel computational tool for automated structure-based drug design. J. Mol. Recog. 1993, 6, 131-137.
    • (1993) J. Mol. Recog. , vol.6 , pp. 131-137
    • Böhm, H.J.1
  • 45
    • 0029444383 scopus 로고
    • A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
    • Jones, G.; Willett, P.; Glen, R. C. A genetic algorithm for flexible molecular overlay and pharmacophore elucidation. J. Comput.-Aided Mol. Des. 1995, 9, 532-549.
    • (1995) J. Comput.-aided Mol. Des. , vol.9 , pp. 532-549
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 46
    • 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.; Murray, C. W.; Auton, T. A.; Paolini, G. V.; Lee, 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. 1997, 11, 425-445.
    • (1997) J. Comput.-aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.1    Murray, C.W.2    Auton, T.A.3    Paolini, G.V.4    Lee, R.P.5
  • 47
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Nemethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C. N.; Paterlini, G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J. Phys. Chem. 1992, 96, 6472-6484.
    • (1992) J. Phys. Chem. , vol.96 , pp. 6472-6484
    • Nemethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 48
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan, R. A.; Totrov, M. M. Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins. J. Mol. Biol. 1994, 235, 983-1002.
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.A.1    Totrov, M.M.2
  • 50
    • 0000504484 scopus 로고    scopus 로고
    • Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure
    • Abagyan, R. A.; Totrov, M. M. Ab Initio Folding of Peptides by the Optimal-Bias Monte Carlo Minimization Procedure. J. Comput. Phys. 1999, 151, 402-421.
    • (1999) J. Comput. Phys. , vol.151 , pp. 402-421
    • Abagyan, R.A.1    Totrov, M.M.2
  • 51
    • 0026681839 scopus 로고
    • Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
    • (a) Abagyan, R. A.; Argos, P. Optimal Protocol and Trajectory Visualization For Conformational Searches of Peptides and Proteins. J. Mol. Biol. 1992, 225, 519-532.
    • (1992) J. Mol. Biol. , vol.225 , pp. 519-532
    • Abagyan, R.A.1    Argos, P.2
  • 52
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • (b) Li, Z.; Scheraga, H. A. Monte Carlo-Minimization Approach to the Multiple-Minima Problem in Protein Folding. PNAS 1987 84, 6611-6615.
    • (1987) PNAS , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 53
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via comprehensive identification and classification of ligand binding envelopes
    • (a) An, J.; Totrov, M.; Abagyan, R. Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics 2005, 4, 752-761.
    • (2005) Mol. Cell. Proteomics , vol.4 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 54
    • 29144482496 scopus 로고    scopus 로고
    • Comprehensive identification of druggable protein ligand binding sites
    • (b) An, J.; Totrov, M.; Abagyan, R. Comprehensive identification of druggable protein ligand binding sites. Genome Inf. 2005, 15, 31-41.
    • (2005) Genome Inf. , vol.15 , pp. 31-41
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 55
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
    • (a) Kramer, B.; Rarey, M.; 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
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 56
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • (b) 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


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