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Volumn 5, Issue 4, 1998, Pages 631-654

A method for biomolecular structural recognition and docking allowing conformational flexibility

Author keywords

Flexible molecular docking and molecular recognition; Geometric Hashing; Hough transform; Induced fit; Object recognition; Structure based drug design

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER SYSTEM; CONFORMATION; CONFORMATIONAL TRANSITION; DRUG DESIGN; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; ROBOTICS;

EID: 0032466036     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1998.5.631     Document Type: Article
Times cited : (60)

References (47)
  • 1
    • 0001635093 scopus 로고
    • The Cambridge Crystallographic Data Center: Computer-based search, retrieval, analyses and display information
    • Allen, F., Bellard, S., Brice, M., et al. 1979. The Cambridge Crystallographic Data Center: computer-based search, retrieval, analyses and display information. Acta Crystallogr. B 35, 2331-2339.
    • (1979) Acta Crystallogr. B , vol.35 , pp. 2331-2339
    • Allen, F.1    Bellard, S.2    Brice, M.3
  • 2
    • 0019397313 scopus 로고
    • Generalizing the Hough transform to detect arbitrary shapes
    • Ballard, D. 1981. Generalizing the Hough transform to detect arbitrary shapes. Pattern Recognition 13(2), 111-122.
    • (1981) Pattern Recognition , vol.13 , Issue.2 , pp. 111-122
    • Ballard, D.1
  • 4
    • 0017411710 scopus 로고
    • The protein data bank: A computer-based archival file for macromolecular structures
    • Bernstein, F., Koetzle, T., Williams, G., et al. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
    • (1977) J. Mol. Biol. , vol.112 , pp. 535-542
    • Bernstein, F.1    Koetzle, T.2    Williams, G.3
  • 5
    • 0020441466 scopus 로고
    • Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution
    • Bolin, J., Filman, D., Matthews, D., Hamlin, R., and Kraut, J. 1982. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. J. Biol. Chem. 257, 13650-13662.
    • (1982) J. Biol. Chem. , vol.257 , pp. 13650-13662
    • Bolin, J.1    Filman, D.2    Matthews, D.3    Hamlin, R.4    Kraut, J.5
  • 8
    • 84986492468 scopus 로고
    • Flexible ligand docking without parameter adjustment across four ligand receptor complexes
    • Clark, K., and Ajay 1995. Flexible ligand docking without parameter adjustment across four ligand receptor complexes. J. Comp. Chem. 16, 1210-1226.
    • (1995) J. Comp. Chem. , vol.16 , pp. 1210-1226
    • Clark, K.1    Ajay2
  • 9
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • Connolly, M. 1983a. Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713.
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.1
  • 10
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly, M. 1983b. Analytical molecular surface calculation. J. Appl. Cryst. 16, 548-558.
    • (1983) J. Appl. Cryst. , vol.16 , pp. 548-558
    • Connolly, M.1
  • 11
    • 0025054246 scopus 로고
    • Structured-based design of nonpeptide inhibitors specific for the human immunodeficiency virus-1 protease
    • DesJarlais, R., Kuntz, I., Furth, P., et al. 1990. Structured-based design of nonpeptide inhibitors specific for the human immunodeficiency virus-1 protease. Proc. Natl. Acad. Sci. U.S.A. 87, 6644-6648.
    • (1990) Proc. Natl. Acad. Sci. U.S.A. , vol.87 , pp. 6644-6648
    • DesJarlais, R.1    Kuntz, I.2    Furth, P.3
  • 12
  • 13
    • 0029025913 scopus 로고
    • A geometry-based suite of molecular docking processes
    • Fischer, D., Lin, S.L., Wolfson, H.J., and Nussinov, R. 1995. A geometry-based suite of molecular docking processes. J. Mol. Biol. 248, 459-477.
    • (1995) J. Mol. Biol. , vol.248 , pp. 459-477
    • Fischer, D.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 14
    • 84988128979 scopus 로고
    • Geometrically feasible binding modes of a flexible ligand molecule at the receptor site
    • Ghose, A., and Crippen, G. 1985. Geometrically feasible binding modes of a flexible ligand molecule at the receptor site. J. Comp. Chem. 6, 350-359.
    • (1985) J. Comp. Chem. , vol.6 , pp. 350-359
    • Ghose, A.1    Crippen, G.2
  • 15
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell, D., and Olson, A., 1990. Automated docking of substrates to proteins by simulated annealing. Proteins Struct. Funct. Genet. 8, 195.
    • (1990) Proteins Struct. Funct. Genet. , vol.8 , pp. 195
    • Goodsell, D.1    Olson, A.2
  • 18
    • 0026310932 scopus 로고
    • Soft docking: Matching of molecular surface cubes
    • Jiang, F., and Kim, S. 1991. Soft docking: matching of molecular surface cubes. J. Mol. Biol. 219, 79-102.
    • (1991) J. Mol. Biol. , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.2
  • 19
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G., Willet, P., and Glen, R. 1995. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245, 43-53.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willet, P.2    Glen, R.3
  • 20
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G., Willett, P., Glen, R., Leach, A., and Taylor, R. 1997. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.3    Leach, A.4    Taylor, R.5
  • 21
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A., Aflalo, C., and Vakser, I. 1992. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc. Natl. Acad. Sci. U.S.A. 89, 2195-2199.
    • (1992) Proc. Natl. Acad. Sci. U.S.A. , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.4    Aflalo, C.5    Vakser, I.6
  • 22
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I. 1992. Structure-based strategies for drug design and discovery. Science 257, 1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.1
  • 23
    • 0020491251 scopus 로고
    • A geometric approach to macromolecule-ligand interactions
    • Kuntz, I., Blaney, J., Oatley, S., Langridge, R., and Ferrin, T. 1982. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288.
    • (1982) J. Mol. Biol. , vol.161 , pp. 269-288
    • Kuntz, I.1    Blaney, J.2    Oatley, S.3    Langridge, R.4    Ferrin, T.5
  • 25
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A. 1994. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235, 345-356.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.1
  • 26
    • 84986467005 scopus 로고
    • Conformational analysis of flexible ligands in macromolecular receptor sites
    • Leach, A., and Kuntz, I. 1992. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Comp. Chem. 13(6), 730-748.
    • (1992) J. Comp. Chem. , vol.13 , Issue.6 , pp. 730-748
    • Leach, A.1    Kuntz, I.2
  • 27
    • 0030130449 scopus 로고    scopus 로고
    • Molecular recognition via the face center representation of molecular surface
    • Lin, S.L., and Nussinov, R. 1996. Molecular recognition via the face center representation of molecular surface. J. Mol. Graphics 14, 78-97.
    • (1996) J. Mol. Graphics , vol.14 , pp. 78-97
    • Lin, S.L.1    Nussinov, R.2
  • 29
    • 0026356149 scopus 로고
    • Computer-assisted rational drug design
    • Martin, Y. 1991, Computer-assisted rational drug design. Methods Enzymol. 203, 587-613.
    • (1991) Methods Enzymol. , vol.203 , pp. 587-613
    • Martin, Y.1
  • 30
    • 0027985242 scopus 로고
    • Rational automatic search method for stable docking models of protein and ligand
    • Mizutani, M., Tomioka, N., and Itai, A. 1994. Rational automatic search method for stable docking models of protein and ligand. J. Mol. Biol. 243, 310-326.
    • (1994) J. Mol. Biol. , vol.243 , pp. 310-326
    • Mizutani, M.1    Tomioka, N.2    Itai, A.3
  • 31
    • 0001520694 scopus 로고
    • Use of structural information in drug design
    • Navia, M., and Murcko, M. 1992. Use of structural information in drug design. Curr. Opin. Struct. Biol. 2, 202-210.
    • (1992) Curr. Opin. Struct. Biol. , vol.2 , pp. 202-210
    • Navia, M.1    Murcko, M.2
  • 32
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional motifs in biological macromolecules by computer vision techniques
    • Nussinov, R., and Wolfson, H.J. 1991. Efficient detection of three-dimensional motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. U.S.A. 88, 10495-10499.
    • (1991) Proc. Natl. Acad. Sci. U.S.A. , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 33
    • 0027235488 scopus 로고
    • Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding proteins with and without a ligand
    • Oh, B., Pandit, J., Kang, C., et al. 1993. Three-dimensional structures of the periplasmic lysine/arginine/ornithine-binding proteins with and without a ligand. J. Biol. Chem. 268, 11348-11355.
    • (1993) J. Biol. Chem. , vol.268 , pp. 11348-11355
    • Oh, B.1    Pandit, J.2    Kang, C.3
  • 34
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using incremental construction algorithm
    • Rarey, M., Kramer, B., Lengauer, T., and Klebe, G. 1996. A fast flexible docking method using incremental construction algorithm. J. Mol. Biol. 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 35
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • Richards, F. 1977. Areas, volumes, packing and protein structure. Annu. Rev. Biophys. Bioeng. 6, 151-176.
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 151-176
    • Richards, F.1
  • 38
    • 0028940058 scopus 로고
    • An automated computer-vision and robotics-based technique for 3-D flexible biomolecular docking and matching
    • Sandak, B., Nussinov, R., and Wolfson, H.J. 1995. An automated computer-vision and robotics-based technique for 3-D flexible biomolecular docking and matching. Comput. Appl. Biosci. 11, 87-99.
    • (1995) Comput. Appl. Biosci. , vol.11 , pp. 87-99
    • Sandak, B.1    Nussinov, R.2    Wolfson, H.J.3
  • 40
    • 0009407367 scopus 로고    scopus 로고
    • Hinge-bending at molecular interfaces: Automated docking of a dihydroxyethylene-containing inhibitor of the HIV-1 protease
    • Sandak, B., Wolfson, H.J., and Nussinov, R. 1996b. Hinge-bending at molecular interfaces: automated docking of a dihydroxyethylene-containing inhibitor of the HIV-1 protease. J. Biomol. Struct. Dyn. 1, 233-252.
    • (1996) J. Biomol. Struct. Dyn. , vol.1 , pp. 233-252
    • Sandak, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 41
    • 0026493924 scopus 로고
    • Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis
    • Sharff, A., Rodseth, L., Spurlino, J., and Quiocho, F. 1992. Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. Biochemistry 31, 10657-10663.
    • (1992) Biochemistry , vol.31 , pp. 10657-10663
    • Sharff, A.1    Rodseth, L.2    Spurlino, J.3    Quiocho, F.4
  • 42
    • 0026209073 scopus 로고
    • Fast drug-receptor mapping by site-directed distances: A novel method of prediciting new pharmacological leads
    • Smellie, A., Crippen, G., and Richards, W. 1991. Fast drug-receptor mapping by site-directed distances: a novel method of prediciting new pharmacological leads. J. Chem. Inform. Comput. Sci. 31, 386-392.
    • (1991) J. Chem. Inform. Comput. Sci. , vol.31 , pp. 386-392
    • Smellie, A.1    Crippen, G.2    Richards, W.3
  • 43
    • 0025754301 scopus 로고
    • The 2.3Å resolution structure of the maltose or maltodextrin binding protein, a primary receptor of bacterial transport and chemotaxis
    • Spurlino, J., Lu, G., and Quiocho, F. 1991. The 2.3Å resolution structure of the maltose or maltodextrin binding protein, a primary receptor of bacterial transport and chemotaxis. J. Biol. Chem. 266, 5202-5219.
    • (1991) J. Biol. Chem. , vol.266 , pp. 5202-5219
    • Spurlino, J.1    Lu, G.2    Quiocho, F.3
  • 44
    • 0027397418 scopus 로고
    • Solution structure of the cyclosporin A/cyclophilin complex by NMR
    • Theriault, Y., Logan, T., Meadows, R., et al. 1993. Solution structure of the cyclosporin A/cyclophilin complex by NMR. Nature 361, 88-94.
    • (1993) Nature , vol.361 , pp. 88-94
    • Theriault, Y.1    Logan, T.2    Meadows, R.3
  • 45
    • 84986532964 scopus 로고
    • Grid-search molecular accessible algorithm for solving the protein docking problem
    • Wang, H. 1991. Grid-search molecular accessible algorithm for solving the protein docking problem. J. Comp. Chem. 12, 746-750.
    • (1991) J. Comp. Chem. , vol.12 , pp. 746-750
    • Wang, H.1
  • 46
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W., Ruppert, J., and Jain, A. 1996. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.3
  • 47
    • 0026301147 scopus 로고
    • Generalizing the generalized Hough transform
    • Wolfson, H.J. 1991. Generalizing the generalized Hough transform. Pattern Recognition Lett. 12(9), 565-573.
    • (1991) Pattern Recognition Lett. , vol.12 , Issue.9 , pp. 565-573
    • Wolfson, H.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.