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Volumn 43, Issue 4, 2003, Pages 1316-1327

BHB: A simple knowledge-based scoring function to improve the efficiency of database screening

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; DATABASE SYSTEMS; HYDROGEN BONDS; THERMODYNAMICS;

EID: 0042199035     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci030006i     Document Type: Article
Times cited : (30)

References (51)
  • 1
    • 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
  • 3
    • 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
  • 4
    • 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
  • 5
    • 0036606204 scopus 로고    scopus 로고
    • ConsDock: A new program for the consensus analysis of protein-ligand interactions
    • Nicodeme. P.; Didier, R. ConsDock: A New Program for the Consensus Analysis of Protein-Ligand Interactions. Proteins 2002, 47, 521-533.
    • (2002) Proteins , vol.47 , pp. 521-533
    • Nicodeme, P.1    Didier, R.2
  • 6
    • 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.; 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. 1997, 11, 425-45.
    • (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
  • 7
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • 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
  • 8
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions; a simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions; a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 9
    • 0033523959 scopus 로고    scopus 로고
    • Predicting binding affinities of protein ligands from three-dimensional models: Application to peptide binding to class I major histocompatibility proteins
    • Rognan, D.; Lauemoller, S. L.; Holm, A.; Buus, S.; Tschinke, V. Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J. Med. Chem. 1999, 42, 4650-4658.
    • (1999) J. Med. Chem. , vol.42 , pp. 4650-4658
    • Rognan, D.1    Lauemoller, S.L.2    Holm, A.3    Buus, S.4    Tschinke, V.5
  • 10
    • 0028454828 scopus 로고
    • The development of a single empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Böhm, H. J. The development of a single empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 8, 243-256.
    • (1994) J. Comput.-Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 12
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work for virtual library screening? An idealized computer experiment
    • Wang, R.; Wang, S. How Does Consensus Scoring Work for Virtual Library Screening? An Idealized Computer Experiment. J. Chem. Inf. Comput. Sci. 2001, 41, 1422-1426.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1422-1426
    • Wang, R.1    Wang, S.2
  • 13
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Wilett, P.; Glen, R. C.; 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    Wilett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 14
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using 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
  • 16
    • 0042430290 scopus 로고    scopus 로고
    • Schrodinger Inc.: Portland, OR
    • Glide 2.0. Schrodinger Inc.: Portland, OR, 2002.
    • (2002) Glide 2.0
  • 17
    • 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, 375-82.
    • (2001) Curr. Opin. Chem. Biol. , vol.5 , pp. 375-382
    • Abagyan, R.1    Totrov, M.2
  • 18
    • 0028854034 scopus 로고
    • Moelcular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G.; Willett, P.; Glen, R. C. Moelcular Recognition of Receptor Sites Using a Genetic Algorithm with a Description of Desolvation. J. Mol. Biol. 1995, 245, 43-53.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 20
    • 0041427871 scopus 로고    scopus 로고
    • Cambridge Crystallographic Data Centre: Cambridge, U.K.
    • GOLD, versions 1.2 and 2.0. Cambridge Crystallographic Data Centre: Cambridge, U.K., 2002.
    • (2002) GOLD, Versions 1.2 and 2.0
  • 21
    • 0033663385 scopus 로고    scopus 로고
    • Modifications of the scoring function in FlexX for virtual screening applications
    • Stahl, M. Modifications of the scoring function in FlexX for virtual screening applications. Perspect. Drug Discovery Des. 2000, 20, 83-98.
    • (2000) Perspect. Drug Discovery Des. , vol.20 , pp. 83-98
    • Stahl, M.1
  • 23
    • 0042931014 scopus 로고    scopus 로고
    • Advanced Chemistry Development Inc.: Toronto, ON
    • ACD logD suite, version 6.00. Advanced Chemistry Development Inc.: Toronto, ON.
    • ACD LogD Suite, Version 6.00
  • 24
    • 0037571112 scopus 로고    scopus 로고
    • The Merck molecular force field. I. Basis, form, scope, parametrization, and performance of MMFF94
    • Halgren, T. A. The Merck Molecular Force Field. I. Basis, Form, Scope, Parametrization, and Performance of MMFF94. J. Comput. Chem. 1996, 17, 490-519.
    • (1996) J. Comput. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 25
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 1990, 112, 6127-6129.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 26
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii
    • Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. The GB/SA Continuum Model for Solvation. A Fast Analytical Method for the Calculation of Approximate Born Radii. J. Phys. Chem. A 1997, 101, 3005-3114.
    • (1997) J. Phys. Chem. A , vol.101 , pp. 3005-3114
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 28
    • 0032226476 scopus 로고    scopus 로고
    • Development of filter functions for protein-ligand docking
    • Stahl, M.; Böhm, H.-J. Development of filter functions for protein-ligand docking. J. Mol. Graph. Model. 1998, 16, 121-132.
    • (1998) J. Mol. Graph. Model. , vol.16 , pp. 121-132
    • Stahl, M.1    Böhm, H.-J.2
  • 30
    • 0037431396 scopus 로고    scopus 로고
    • De Novo design, synthesis and evaluation of novel non-steroidal high affinity ligands for the estrogen receptor
    • Schmidt, J. M.; Mercure, J. A.; Feher, M.; Dunn-Dufault, R.; Peter, M. G.; Redden, P. R. De Novo Design, Synthesis and Evaluation of Novel Non-Steroidal High Affinity Ligands for the Estrogen Receptor. J. Med. Chem. 2003, 46, 1408-1418.
    • (2003) J. Med. Chem. , vol.46 , pp. 1408-1418
    • Schmidt, J.M.1    Mercure, J.A.2    Feher, M.3    Dunn-Dufault, R.4    Peter, M.G.5    Redden, P.R.6
  • 32
    • 0035865781 scopus 로고    scopus 로고
    • Improved scoring of ligand-protein interactions using OWFEG energy grids
    • Pearlman, D. A.; Charifson, P. S. Improved Scoring of Ligand-Protein Interactions Using OWFEG Energy Grids. J. Med. Chem. 2001, 44, 502-511.
    • (2001) J. Med. Chem. , vol.44 , pp. 502-511
    • Pearlman, D.A.1    Charifson, P.S.2
  • 33
    • 0042430285 scopus 로고    scopus 로고
    • last accessed 16.10.2002
    • http://www.schrodinger.com/docs/impact2.0/pdf/tech_notes/tech_notes.pdf, (last accessed 16.10.2002).
  • 34
    • 0041427872 scopus 로고    scopus 로고
    • note
    • The decoy set was kindly provided by Dr. Tom Halgren, Schrodinger Inc., for the evaluation of the Glide program and its comparison with other approaches.
  • 35
    • 0031059270 scopus 로고    scopus 로고
    • The estradiol pharmacophore: Ligand structure - Estrogen receptor binding affinity relationships and a model for the estrogen receptor binding site
    • Anstead, G. M.; Carlson, K. E.; Katzenellenbogen, J. A. The estradiol pharmacophore: Ligand structure - estrogen receptor binding affinity relationships and a model for the estrogen receptor binding site. Steroids 1997, 62, 268-298.
    • (1997) Steroids , vol.62 , pp. 268-298
    • Anstead, G.M.1    Carlson, K.E.2    Katzenellenbogen, J.A.3
  • 36
    • 0034121290 scopus 로고    scopus 로고
    • Androgen receptor anatagonists (antiandrogens): Structure activity relationships
    • Singh, S. M.; Gauthier, S.; Labrie, F. Androgen Receptor Anatagonists (Antiandrogens): Structure Activity Relationships. Curr. Med. Chem. 2000, 7, 211-247.
    • (2000) Curr. Med. Chem. , vol.7 , pp. 211-247
    • Singh, S.M.1    Gauthier, S.2    Labrie, F.3
  • 37
    • 0034121721 scopus 로고    scopus 로고
    • The structure of inosine 5′-monophosphate dehydrogenase and the design of novel inhibitors
    • Sintchak, M. D.; Nimmesgern, E. The structure of inosine 5′-monophosphate dehydrogenase and the design of novel inhibitors. Immunopharmacology 2000, 47, 163-184.
    • (2000) Immunopharmacology , vol.47 , pp. 163-184
    • Sintchak, M.D.1    Nimmesgern, E.2
  • 38
    • 0034473229 scopus 로고    scopus 로고
    • Characterisation of the affinity of different anabolics and synthetic hormones to the human androgen receptor, human sex hormone binding globulin and to the bovine progestin receptor
    • Bauer, E. R. S.; Daxenberger, A.; Petri, T.; Sauerwein, H.; Meyer, H. H. D. Characterisation of the affinity of different anabolics and synthetic hormones to the human androgen receptor, human sex hormone binding globulin and to the bovine progestin receptor. Acta Pathol. Microbiol. Immunol. Scand. 2000, 108, 838-846.
    • (2000) Acta Pathol. Microbiol. Immunol. Scand. , vol.108 , pp. 838-846
    • Bauer, E.R.S.1    Daxenberger, A.2    Petri, T.3    Sauerwein, H.4    Meyer, H.H.D.5
  • 40
    • 0036189788 scopus 로고    scopus 로고
    • The ligand binding profiles of estrogen receptors alpha and beta are species dependent
    • Harris, H. A.; Bapat, A. R.; Gonder, D. S.; Frail, D. E. The ligand binding profiles of estrogen receptors alpha and beta are species dependent. Steroids 2002, 67, 379-384.
    • (2002) Steroids , vol.67 , pp. 379-384
    • Harris, H.A.1    Bapat, A.R.2    Gonder, D.S.3    Frail, D.E.4
  • 41
    • 0031911783 scopus 로고    scopus 로고
    • Mutations in a conserved residue in the influenza virus neuraminidase active site decrease sensitivity to Neu5Ac2en-derived inhibitors
    • McKimm-Breschkin, J. L.; Sahasrabudhe, A.; Blick, T. J.; McDonald, M.; Colman, P. M.; Hart, G. J.; Bethell, R. C.; Varghese, J. N. Mutations in a Conserved Residue in the Influenza virus Neuraminidase Active Site Decrease Sensitivity to Neu5Ac2en-derived Inhibitors. J. Virol. 1998, 72, 2456-2462.
    • (1998) J. Virol. , vol.72 , pp. 2456-2462
    • McKimm-Breschkin, J.L.1    Sahasrabudhe, A.2    Blick, T.J.3    McDonald, M.4    Colman, P.M.5    Hart, G.J.6    Bethell, R.C.7    Varghese, J.N.8
  • 42
    • 0032510373 scopus 로고    scopus 로고
    • Dihydropyrancarboxamides related to zanamivir: A new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B
    • Taylor, N. R.; Cleasby, A.; Singh, O.; Skarzynski, T.; Wonacott, A. J.; Smith, P. W.; Sollis, S. L.; Howes, P. D.; Cherry, P. C.; Bethell, R.; Colman, P.; Varghese, J. Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 2. Crystallographic and molecular modeling study of complexes of 4-amino-4H-pyran-6-carboxamides and sialidase from influenza virus types A and B. J. Med. Chem. 1998, 41, 798-807.
    • (1998) J. Med. Chem. , vol.41 , pp. 798-807
    • Taylor, N.R.1    Cleasby, A.2    Singh, O.3    Skarzynski, T.4    Wonacott, A.J.5    Smith, P.W.6    Sollis, S.L.7    Howes, P.D.8    Cherry, P.C.9    Bethell, R.10    Colman, P.11    Varghese, J.12
  • 43
    • 0025162702 scopus 로고
    • A pro to gly mutation in the arabinose-binding protein enhances and alters specificity
    • Vermersch, P. S.; Tesmer, J. G.; Lemon, D. D.; Quiocho, F. A. A Pro to Gly Mutation in the Arabinose-binding Protein Enhances and Alters Specificity. J. Biol. Chem. 1990, 265, 16592-16603.
    • (1990) J. Biol. Chem. , vol.265 , pp. 16592-16603
    • Vermersch, P.S.1    Tesmer, J.G.2    Lemon, D.D.3    Quiocho, F.A.4
  • 44


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