메뉴 건너뛰기




Volumn 33, Issue 3, 1998, Pages 367-382

Flexible docking using Tabu search and an empirical estimate of binding affinity

Author keywords

Binding affinity prediction; Empirical scoring function; Ligand protein docking; Molecular recognition; Tabu search

Indexed keywords

ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; CLUSTER ANALYSIS; COMPLEX FORMATION; CRYSTAL STRUCTURE; DATA BASE; EMPIRICISM; ENTROPY; LIGAND BINDING; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; RECEPTOR OCCUPANCY; REGRESSION ANALYSIS; SCORING SYSTEM;

EID: 0032533791     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981115)33:3<367::AID-PROT6>3.0.CO;2-W     Document Type: Article
Times cited : (372)

References (40)
  • 1
    • 0001650642 scopus 로고
    • A good ligand is hard to find: Automatic docking methods
    • Blaney, J.M., Dixon, J.S. A good ligand is hard to find: Automatic docking methods. Perspect. Drug Discov. Res. 1:301-319, 1993.
    • (1993) Perspect. Drug Discov. Res. , vol.1 , pp. 301-319
    • Blaney, J.M.1    Dixon, J.S.2
  • 2
    • 0028882706 scopus 로고
    • Docking small-molecule ligands into active sites
    • Jones, G., Willett, P. Docking small-molecule ligands into active sites. Curr. Opin. Biotech. 6:652-656, 1995.
    • (1995) Curr. Opin. Biotech. , vol.6 , pp. 652-656
    • Jones, G.1    Willett, P.2
  • 3
    • 0029062909 scopus 로고
    • Ligand-protein docking and rational drug design
    • Lybrand, T.P. Ligand-protein docking and rational drug design. Curr. Opin. Struct. Biol. 5:224-228, 1995.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 224-228
    • Lybrand, T.P.1
  • 6
    • 0029902763 scopus 로고    scopus 로고
    • Computational methods for biomolecular docking
    • Lengauer, T., Rarey, M. Computational methods for biomolecular docking. Curr. Opin. Struct. Biol. 6:402-406, 1996.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 402-406
    • Lengauer, T.1    Rarey, M.2
  • 8
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G., Willett, P., Glen, R.C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245:43-53, 1995.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 9
    • 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., Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267:727-748, 1997.
    • (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
  • 10
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A.R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235:345-356, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 11
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D.S., Olson, A.J. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202, 1990.
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 12
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Morris, G.M., Goodsell, D.S., Huey, R., Olson, A.J. Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des. 10:293-304, 1996.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 13
    • 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., et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming. Chem. Biol. 2:317-324, 1995.
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3
  • 15
    • 43949148576 scopus 로고
    • A genetic algorithm method for molecular docking flexible molecules
    • Judson, R.S., Jaeger, E.P., Treasurywala, A.M. A genetic algorithm method for molecular docking flexible molecules. J. Mol. Struct. 308:191-206, 1994.
    • (1994) J. Mol. Struct. , vol.308 , pp. 191-206
    • Judson, R.S.1    Jaeger, E.P.2    Treasurywala, A.M.3
  • 17
    • 84986492468 scopus 로고
    • Flexible ligand docking without parameter adjustment across four ligand-receptor complexes
    • Clark, K.P., Ajay. Flexible ligand docking without parameter adjustment across four ligand-receptor complexes. J. Comp. Chem. 16:1210-1226, 1995.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1210-1226
    • Clark, K.P.1    Ajay2
  • 18
    • 84986467005 scopus 로고
    • The conformational analysis of flexible ligands in macromolecular receptor sites
    • Leach, A.R., Kuntz, I.D. The conformational analysis of flexible ligands in macromolecular receptor sites. J. Comp. Chem. 13:730-748, 1992.
    • (1992) J. Comp. Chem. , vol.13 , pp. 730-748
    • Leach, A.R.1    Kuntz, I.D.2
  • 19
    • 0030599010 scopus 로고    scopus 로고
    • Predicting receptor-ligand interactions by an incremental construction algorithm
    • Rarey, M., Kramer, B., Lengauer, T., Klebe, G. Predicting receptor-ligand interactions by an incremental construction algorithm. J. Mol. Biol. 261:470-489, 1996.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 20
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W., Ruppert, J., Jain, A.N. Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 3:449-462, 1996.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 21
    • 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. 11:333-344, 1997.
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 22
    • 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. 8:153-174, 1994.
    • (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
  • 23
    • 0028455325 scopus 로고
    • Evaluating docked complexes with the HINT exponential functions and empirical atomic hydrophobicities
    • Meng, E.C., Kuntz, I.D., Abraham, D.J., Kellogg, G.E. Evaluating docked complexes with the HINT exponential functions and empirical atomic hydrophobicities. J. Comput Aided Mol. Des. 8:299-306, 1994.
    • (1994) J. Comput Aided Mol. Des. , vol.8 , pp. 299-306
    • Meng, E.C.1    Kuntz, I.D.2    Abraham, D.J.3    Kellogg, G.E.4
  • 24
    • 0031592453 scopus 로고    scopus 로고
    • Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearest-neighbours genetic algorithm
    • Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., Kuhn, L.A. Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearest-neighbours genetic algorithm. J. Mol. Biol. 265:445-464, 1997.
    • (1997) J. Mol. Biol. , vol.265 , pp. 445-464
    • Raymer, M.L.1    Sanschagrin, P.C.2    Punch, W.F.3    Venkataraman, S.4    Goodman, E.D.5    Kuhn, L.A.6
  • 25
    • 0031135364 scopus 로고    scopus 로고
    • A comparison of heuristic search algorithms for molecular docking
    • Westhead, D.R., Clark, D.E., Murray, C.W. A comparison of heuristic search algorithms for molecular docking. J. Comput. Aided Mol. Des. 11:209-228, 1997.
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 209-228
    • Westhead, D.R.1    Clark, D.E.2    Murray, C.W.3
  • 27
    • 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. 11:425-445, 1997.
    • (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
  • 28
    • 0028454828 scopus 로고
    • The development of a simple 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 simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8:243-256, 1994.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.-J.1
  • 29
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • Jain, A.J. Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities. J. Comput. Aided Mol. Des. 10:427-440, 1996.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 427-440
    • Jain, A.J.1
  • 30
    • 0017411710 scopus 로고
    • The Protein Data Bank: A computer-based archival file for macromolecular structures
    • Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., et al. The Protein Data Bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
    • (1977) J. Mol. Biol. , vol.112 , pp. 535-542
    • Bernstein, F.C.1    Koetzle, T.F.2    Williams, G.J.B.3
  • 31
    • 2342652962 scopus 로고    scopus 로고
    • San Diego, CA: Molecular Simulations Inc.
    • InsightII/Discover, v. 95.0. San Diego, CA: Molecular Simulations Inc., 1996.
    • (1996) InsightII/Discover, V. 95.0
  • 32
    • 0023965741 scopus 로고
    • SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules
    • Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci. 28:31-36, 1988.
    • (1988) J. Chem. Inf. Comput. Sci. , vol.28 , pp. 31-36
    • Weininger, D.1
  • 33
    • 84986522918 scopus 로고
    • ICM - A new method for protein modelling and design: Applications to docking and structure prediction from distorted native conformation
    • Abagyan, R.A., Totrov, M., Kuznetsov D. ICM - a new method for protein modelling and design: Applications to docking and structure prediction from distorted native conformation. J. Comp. Chem. 15:488-506, 1994.
    • (1994) J. Comp. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.A.1    Totrov, M.2    Kuznetsov, D.3
  • 35
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
    • Head, R.D., Smythe, M.L., Oprea, T.I., Waller, C.L., Green, S.M., Marshall, G.R. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J. Am. Chem. Soc. 118:3959-3969, 1996.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 36
    • 0024356436 scopus 로고
    • Crystal structure of rat intestinal fatty-acid-binding protein
    • Sacchettini, J.C., Gordon, J.I., Banaszak, L.J. Crystal structure of rat intestinal fatty-acid-binding protein. J. Mol. Biol. 208:327-339, 1989.
    • (1989) J. Mol. Biol. , vol.208 , pp. 327-339
    • Sacchettini, J.C.1    Gordon, J.I.2    Banaszak, L.J.3
  • 37
    • 0026606240 scopus 로고
    • Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin
    • Weber, P.C., Wendoloski, J.J., Pantoliano, M.W., Salemme, F.R. Crystallographic and thermodynamic comparison of natural and synthetic ligands bound to streptavidin. J. Am. Chem. Soc. 114:3197-3200, 1992.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3197-3200
    • Weber, P.C.1    Wendoloski, J.J.2    Pantoliano, M.W.3    Salemme, F.R.4
  • 39
    • 13344275187 scopus 로고    scopus 로고
    • Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase
    • Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E., et al. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat. Struct. Biol. 3:233-239, 1996.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 233-239
    • Strynadka, N.C.J.1    Eisenstein, M.2    Katchalski-Katzir, E.3
  • 40
    • 0031181870 scopus 로고    scopus 로고
    • Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention
    • Rarey, M., Kramer, B., Lengauer, T., Klebe, G. Multiple automatic base selection: Protein-ligand docking based on incremental construction without manual intervention. J. Comput. Aided Mol. Des. 11:369-384, 1997.
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 369-384
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.