메뉴 건너뛰기




Volumn 48, Issue 19, 2005, Pages 6012-6022

Fast structure-based virtual ligand screening combining FRED, DOCK, and surflex

Author keywords

[No Author keywords available]

Indexed keywords

1,3,5(10) ESTRATRIEN 3,11ALPHA DIOL 17 ONE 11ALPHA HEMISUCCINATE; 2 [3 (4 CARBAMIMIDOYLPHENYL)UREIDO] N [1 (3 OXO 3,4 DIHYDRO 2H BENZO[1,4]OXAZIN 6 YL)ETHYL]ACETAMIDE; 4 ACETAMIDO 3 GUANIDINOBENZOIC ACID; 7 O [2 (1,3 DIOXANYL)ETHYL] 3 (4 HYDROXYPHENYL) 4H 1 BENZOPYRAN 4 ONE; ASCORBIGEN; BLOOD CLOTTING FACTOR 7; ESTROGEN RECEPTOR; LIGAND; NAFOXIDENE; NEW DRUG; SIALIDASE; THYMIDINE KINASE; UNCLASSIFIED DRUG; [4 [(1 HYDROXYL 3 OXO 6,7 DIHYDRO 3H,5H PYRIDO[3,2,1 IJ]QUINOLINE 2 CARBONYL)AMINO]PHENYL]ACETIC ACID;

EID: 24944433024     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm050262h     Document Type: Article
Times cited : (111)

References (53)
  • 1
    • 0036007208 scopus 로고    scopus 로고
    • Virtual screening and fast automated docking methods
    • Schneider, G.; Bohm, 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    Bohm, H.J.2
  • 2
    • 0037107887 scopus 로고    scopus 로고
    • Structure-based virtual screening: An overview
    • 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
  • 3
    • 2942667923 scopus 로고    scopus 로고
    • Ligand identification for G-protein-coupled receptors: A lead generation perspective
    • Bleicher, K. H.; Green, L. G.; Martin, R. E.; Rogers-Evans, M. Ligand identification for G-protein-coupled receptors: a lead generation perspective. Curr. Opin. Chem. Biol. 2004, 8, 287-296.
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 287-296
    • Bleicher, K.H.1    Green, L.G.2    Martin, R.E.3    Rogers-Evans, M.4
  • 6
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. L. The many roles of computation in drug discovery. Science 2004, 303, 1813-1818.
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 7
    • 0035416126 scopus 로고    scopus 로고
    • High-throughput docking for lead generation
    • 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
  • 8
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • Shoichet, B. K. Virtual screening of chemical libraries. Nature 2004, 432, 862-865.
    • (2004) Nature , vol.432 , pp. 862-865
    • Shoichet, B.K.1
  • 9
    • 2542631937 scopus 로고    scopus 로고
    • Virtual screening for inhibitors of human aldose reductase
    • Kraemer, O.; Hazemann, I.; Podjarny, A. D.; Klebe, G. Virtual screening for inhibitors of human aldose reductase. Proteins 2004, 55, 814-823.
    • (2004) Proteins , vol.55 , pp. 814-823
    • Kraemer, O.1    Hazemann, I.2    Podjarny, A.D.3    Klebe, G.4
  • 10
    • 8544230644 scopus 로고    scopus 로고
    • GAsDock: A new approach for rapid fexible docking based on an improved multi-population genetic algorithm
    • Li, H.; Li, C.; Gui, C.; Luo, X.; Chen, K. et al. GAsDock: a new approach for rapid fexible docking based on an improved multi-population genetic algorithm. Bioorg. Med. Chem. Lett. 2004, 14, 4671-4676.
    • (2004) Bioorg. Med. Chem. Lett. , vol.14 , pp. 4671-4676
    • Li, H.1    Li, C.2    Gui, C.3    Luo, X.4    Chen, K.5
  • 11
    • 6344294057 scopus 로고    scopus 로고
    • FlexX-Scan: Fast, structure-based virtual screening
    • Schellhammer, I.; Rarey, M. FlexX-Scan: fast, structure-based virtual screening. Proteins 2004, 57, 504-517.
    • (2004) Proteins , vol.57 , pp. 504-517
    • Schellhammer, I.1    Rarey, M.2
  • 12
    • 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 2004, 57, 225-242.
    • (2004) Proteins , vol.57 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4
  • 13
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • 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
  • 15
    • 0038185582 scopus 로고    scopus 로고
    • Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
    • 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.
    • (2003) J. Mol. Model. (Online) , vol.9 , pp. 47-57
    • Schulz-Gasch, T.1    Stahl, M.2
  • 16
    • 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
  • 17
    • 0038205821 scopus 로고    scopus 로고
    • Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in scoring function design
    • Smith, R.; Hubbard, R. E.; Gschwend, D. A.; Leach, A. R.; Good, A. C. Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in scoring function design. J. Mol. Graphics Modell. 2003, 22, 41-53.
    • (2003) J. Mol. Graphics Modell. , vol.22 , pp. 41-53
    • Smith, R.1    Hubbard, R.E.2    Gschwend, D.A.3    Leach, A.R.4    Good, A.C.5
  • 18
    • 12444278563 scopus 로고    scopus 로고
    • Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: Mapping a pharmacophore for success
    • Good, A. C.; Cheney, D. L.; Sitkoff, D. F.; Tokarski, J. S.; Stouch, T. R. et al. Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: mapping a pharmacophore for success. J. Mol. Graphics Modell. 2003, 22, 31-40.
    • (2003) J. Mol. Graphics Modell. , vol.22 , pp. 31-40
    • Good, A.C.1    Cheney, D.L.2    Sitkoff, D.F.3    Tokarski, J.S.4    Stouch, T.R.5
  • 19
    • 0038544571 scopus 로고    scopus 로고
    • Analysis and optimization of structure-based virtual screening protocols (1): Exploration of ligand conformational sampling techniques
    • Good, A. C.; Cheney, D. L. Analysis and optimization of structure-based virtual screening protocols (1): exploration of ligand conformational sampling techniques. J. Mol. Graphics Modell. 2003, 22, 23-30.
    • (2003) J. Mol. Graphics Modell. , vol.22 , pp. 23-30
    • Good, A.C.1    Cheney, D.L.2
  • 20
    • 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
  • 21
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
    • (1999) J. Med. Chem. , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 22
    • 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
  • 23
    • 4644235643 scopus 로고    scopus 로고
    • Virtual screening in lead discovery and optimization
    • Jain, A. N. Virtual screening in lead discovery and optimization. Curr. Opin. Drug Discovery Dev. 2004, 7, 396-403.
    • (2004) Curr. Opin. Drug Discovery Dev. , vol.7 , pp. 396-403
    • Jain, A.N.1
  • 26
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I. D. Structure-based strategies for drug design and discovery. Science 1992, 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.D.1
  • 27
    • 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. 2003, 46, 499-511.
    • (2003) J. Med. Chem. , vol.46 , pp. 499-511
    • Jain, A.N.1
  • 28
    • 0141545126 scopus 로고    scopus 로고
    • Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening
    • Peng, H.; Huang, N.; Qi, J.; Xie, P.; Xu, C. et al. Identification of novel inhibitors of BCR-ABL tyrosine kinase via virtual screening. Bioorg. Med. Chem. Lett. 2003, 13, 3693-3699.
    • (2003) Bioorg. Med. Chem. Lett. , vol.13 , pp. 3693-3699
    • Peng, H.1    Huang, N.2    Qi, J.3    Xie, P.4    Xu, C.5
  • 29
    • 12144289984 scopus 로고    scopus 로고
    • Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
    • Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J. et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
    • (2004) J. Med. Chem. , vol.47 , pp. 1739-1749
    • Friesner, R.A.1    Banks, J.L.2    Murphy, R.B.3    Halgren, T.A.4    Klicic, J.J.5
  • 30
    • 0347296066 scopus 로고    scopus 로고
    • Assessing the performance of OMEGA with respect to retrieving bioactive conformations
    • Bostrom, J.; Greenwood, J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J. Mol. Graphics Modell. 2003, 21, 449-462.
    • (2003) J. Mol. Graphics Modell. , vol.21 , pp. 449-462
    • Bostrom, J.1    Greenwood, J.R.2    Gottfries, J.3
  • 31
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
    • (2004) J. Med. Chem. , vol.47 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 32
    • 0033550314 scopus 로고    scopus 로고
    • Novel aromatic inhibitors of influenza virus neuraminidase make selective interactions with conserved residues and water molecules in the active site
    • Finley, J. B.; Atigadda, V. R.; Duarte, F.; Zhao, J. J.; Brouillette, W. J. et al. Novel aromatic inhibitors of influenza virus neuraminidase make selective interactions with conserved residues and water molecules in the active site. J. Mol. Biol. 1999, 293, 1107-1119.
    • (1999) J. Mol. Biol. , vol.293 , pp. 1107-1119
    • Finley, J.B.1    Atigadda, V.R.2    Duarte, F.3    Zhao, J.J.4    Brouillette, W.J.5
  • 33
    • 0028940702 scopus 로고
    • Structures of aromatic inhibitors of influenza virus neuraminidase
    • Jedrzejas, M. J.; Singh, S.; Brouillette, W. J.; Laver, W. G.; Air, G. M. et al. Structures of aromatic inhibitors of influenza virus neuraminidase. Biochemistry 1995, 34, 3144-3151.
    • (1995) Biochemistry , vol.34 , pp. 3144-3151
    • Jedrzejas, M.J.1    Singh, S.2    Brouillette, W.J.3    Laver, W.G.4    Air, G.M.5
  • 34
    • 16644374078 scopus 로고    scopus 로고
    • A benzole acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase
    • Lommer, B. S.; Ali, S. M.; Bajpai, S. N.; Brouillette, W. J.; Air, G. M. et al. A benzole acid inhibitor induces a novel conformational change in the active site of Influenza B virus neuraminidase. Acta Crystallogr. D Biol. Crystallogr. 2004, 60, 1017-1023.
    • (2004) Acta Crystallogr. D Biol. Crystallogr. , vol.60 , pp. 1017-1023
    • Lommer, B.S.1    Ali, S.M.2    Bajpai, S.N.3    Brouillette, W.J.4    Air, G.M.5
  • 36
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W.; Ruppert, J.; Jain, A. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.3
  • 37
    • 0028925854 scopus 로고
    • A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies
    • White, C. L.; Janakiraman, M. N.; Laver, W. G.; Philippon, C.; Vasella, A. et al. A sialic acid-derived phosphonate analog inhibits different strains of influenza virus neuraminidase with different efficiencies. J. Mol. Biol. 1995, 245, 623-634.
    • (1995) J. Mol. Biol. , vol.245 , pp. 623-634
    • White, C.L.1    Janakiraman, M.N.2    Laver, W.G.3    Philippon, C.4    Vasella, A.5
  • 38
    • 0037451846 scopus 로고    scopus 로고
    • Design, synthesis, and structure-activity relationship of a new class of amidinophenylurea-based factor VIIa inhibitors
    • Klingler, O.; Matter, H.; Schudok, M.; Bajaj, S. P.; Czech, J. et al. Design, synthesis, and structure-activity relationship of a new class of amidinophenylurea-based factor VIIa inhibitors. Bioorg. Med. Chem. Lett. 2003, 13, 1463-1467.
    • (2003) Bioorg. Med. Chem. Lett. , vol.13 , pp. 1463-1467
    • Klingler, O.1    Matter, H.2    Schudok, M.3    Bajaj, S.P.4    Czech, J.5
  • 39
    • 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. et al. 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
  • 40
    • 0346731234 scopus 로고    scopus 로고
    • HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases
    • Floriano, W. B.; Vaidehi, N.; Zamanakos, G.; Goddard, W. A., 3rd HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. J. Med. Chem. 2004, 47, 56-71.
    • (2004) J. Med. Chem. , vol.47 , pp. 56-71
    • Floriano, W.B.1    Vaidehi, N.2    Zamanakos, G.3    Goddard III, W.A.4
  • 41
    • 17144414125 scopus 로고    scopus 로고
    • Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
    • Wang, J.; Kang, X.; Kuntz, I. D.; Kollman, P. A. Hierarchical Database Screenings for HIV-1 Reverse Transcriptase Using a Pharmacophore Model, Rigid Docking, Solvation Docking, and MM-PB/SA. J. Med. Chem. 2005, 48, 2432-2444.
    • (2005) J. Med. Chem. , vol.48 , pp. 2432-2444
    • Wang, J.1    Kang, X.2    Kuntz, I.D.3    Kollman, P.A.4
  • 42
    • 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.; Waldman, F. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graphics Modell. 2003, 21, 289-307.
    • (2003) J. Mol. Graphics Modell. , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, F.4
  • 44
    • 17144373303 scopus 로고    scopus 로고
    • Druggability indices for protein targets derived from NMR-based screening data
    • Hajduk, P. J.; Huth, J. R.; Fesik, S. W. Druggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 2005, 48, 2518-2525.
    • (2005) J. Med. Chem. , vol.48 , pp. 2518-2525
    • Hajduk, P.J.1    Huth, J.R.2    Fesik, S.W.3
  • 45
    • 2342514226 scopus 로고    scopus 로고
    • Guided docking approaches to structure-based design and screening
    • Fradera, X.; Mestres, J. Guided docking approaches to structure-based design and screening. Curr. Top. Med. Chem. 2004, 4, 687-700.
    • (2004) Curr. Top. Med. Chem. , vol.4 , pp. 687-700
    • Fradera, X.1    Mestres, J.2
  • 46
    • 0037763817 scopus 로고    scopus 로고
    • Comparative analysis of 11 scoring functions for molecular docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative analysis of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2307.
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2307
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 50
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan, R.; Totrov, 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.1    Totrov, M.2
  • 51
    • 84988053694 scopus 로고
    • An all atom force field for simulations of proteins and nucleic acids
    • Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230-252.
    • (1986) J. Comput. Chem. , vol.7 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4
  • 52
    • 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
  • 53
    • 0023936327 scopus 로고
    • Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
    • DesJarlais, R. L.; Sheridan, R. P.; Seibel, G. L.; Dixon, J. S.; Kuntz, I. D. et al. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 1988, 31, 722-729.
    • (1988) J. Med. Chem. , vol.31 , pp. 722-729
    • DesJarlais, R.L.1    Sheridan, R.P.2    Seibel, G.L.3    Dixon, J.S.4    Kuntz, I.D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.