메뉴 건너뛰기




Volumn 6, Issue 3, 1996, Pages 402-406

Computational methods for biomolecular docking

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; COMPUTER ANALYSIS; ENERGY; LIGAND BINDING; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN INTERACTION; SHORT SURVEY;

EID: 0029902763     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(96)80061-3     Document Type: Article
Times cited : (651)

References (46)
  • 1
    • 0027976930 scopus 로고
    • Molecular surface representation by sparse critical points
    • Lin LS, Nussinov R, Fischer D, Wolfson H: Molecular surface representation by sparse critical points. Proteins 1994, 18:94-101.
    • (1994) Proteins , vol.18 , pp. 94-101
    • Lin, L.S.1    Nussinov, R.2    Fischer, D.3    Wolfson, H.4
  • 2
    • 0029089732 scopus 로고
    • Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed sparse points in docking
    • Norel R, Lin SL, Wolfson HL, Nussinov R: Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed sparse points in docking. J Mol Biol 1995, 252:263-273.
    • (1995) J Mol Biol , vol.252 , pp. 263-273
    • Norel, R.1    Lin, S.L.2    Wolfson, H.L.3    Nussinov, R.4
  • 3
    • 0028575449 scopus 로고
    • Hydrophobic docking: A proposed enhancement to molecular recognition techniques
    • Vakser IA, Aflalo C: Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 1994, 20:320-329.
    • (1994) Proteins , vol.20 , pp. 320-329
    • Vakser, I.A.1    Aflalo, C.2
  • 5
    • 0026310932 scopus 로고
    • Soft docking: Matching of molecular surface cubes
    • Jiang F, Kim S: Soft docking: matching of molecular surface cubes. J Mol Biol 1991, 219:79-102.
    • (1991) J Mol Biol , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.2
  • 6
    • 0026464639 scopus 로고
    • New algorithm to model protein-protein recognition based on surface complementarity
    • Walls PH, Sternberg MJE: New algorithm to model protein-protein recognition based on surface complementarity. J Mol Biol 1992, 228:277-297.
    • (1992) J Mol Biol , vol.228 , pp. 277-297
    • Walls, P.H.1    Sternberg, M.J.E.2
  • 7
    • 0027958638 scopus 로고
    • PUZZLE: A new method for automated protein docking based on surface shape complementarity
    • Helmer-Citterich M, Tramontano A: PUZZLE: a new method for automated protein docking based on surface shape complementarity. J Mol Biol 1994, 235:1021-1031.
    • (1994) J Mol Biol , vol.235 , pp. 1021-1031
    • Helmer-Citterich, M.1    Tramontano, A.2
  • 10
    • 0029025913 scopus 로고
    • A geometry-based suite of molecular docking processes
    • Fischer D, Lin SL, Wolfson HL, Nussinov R: A geometry-based suite of molecular docking processes. J Mol Biol 1995, 248:459-477.
    • (1995) J Mol Biol , vol.248 , pp. 459-477
    • Fischer, D.1    Lin, S.L.2    Wolfson, H.L.3    Nussinov, R.4
  • 12
    • 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 AA, Aflalo C, Vakser IA: Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992, 89:2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 13
    • 0028984540 scopus 로고
    • Protein docking for low-resolution structures
    • Vakser IA: Protein docking for low-resolution structures. Protein Eng 1995, 8:371-377.
    • (1995) Protein Eng , vol.8 , pp. 371-377
    • Vakser, I.A.1
  • 14
    • 0028410583 scopus 로고
    • Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy
    • Totrov M, Abagyan R: Detailed ab initio prediction of lysozyme-antibody complex with 1.6 Å accuracy. Nat Struct Biol 1994, 1:259-263.
    • (1994) Nat Struct Biol , vol.1 , pp. 259-263
    • Totrov, M.1    Abagyan, R.2
  • 15
    • 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
  • 16
    • 0029022714 scopus 로고
    • Potential energy functions
    • Halgren TA: Potential energy functions. Curr Opin Struct Biol 1995, 5:205-210.
    • (1995) Curr Opin Struct Biol , vol.5 , pp. 205-210
    • Halgren, T.A.1
  • 17
    • 0028412035 scopus 로고
    • FLOG: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
    • Miller MD, Kearsley SK, Underwood DJ, Sheridan RP: FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 1994, 8:153-174.
    • (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
  • 19
    • 0028522365 scopus 로고
    • A fast and efficient method to generate biologically relevant conformations
    • Klebe G, Mietzner T: A fast and efficient method to generate biologically relevant conformations. J Comput Aided Mol Des 1994, 8:583-606.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 583-606
    • Klebe, G.1    Mietzner, T.2
  • 20
    • 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 HJ: 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 1994, 8:243-256.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 243-256
    • Böhm, H.J.1
  • 21
    • 84986467005 scopus 로고
    • Conformational analysis of flexible ligands in macromolecular receptor sites
    • Leach AR, Kuntz ID: 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
  • 22
    • 0027985242 scopus 로고
    • Rational automatic search method for stable docking models of protein and ligand
    • Mizutani MY, Tomioka N, Itai A: Rational automatic search method for stable docking models of protein and ligand. J Mol Biol 1994, 243:310-326.
    • (1994) J Mol Biol , vol.243 , pp. 310-326
    • Mizutani, M.Y.1    Tomioka, N.2    Itai, A.3
  • 23
    • 0029197510 scopus 로고
    • Time-efficient docking of flexible ligands into active sites of proteins
    • Edited by Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S. Menlo Park, CA: AAAI Press
    • Rarey M, Kramer B, Lengauer T: Time-efficient docking of flexible ligands into active sites of proteins. In Proceedings of the Third International Conference on Intelligent Systems in Molecular Biology. Edited by Rawlings C, Clark D, Altman R, Hunter L, Lengauer T, Wodak S. Menlo Park, CA: AAAI Press; 1995:300-308.
    • (1995) Proceedings of the Third International Conference on Intelligent Systems in Molecular Biology , pp. 300-308
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 24
    • 0028940058 scopus 로고
    • An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching
    • Sandak B, Nussinov R, Wolfson HJ: An automated computer vision and robotics-based technique for 3-D flexible biomolecular docking and matching. Comput Appl Biosci 1995, 11:87-99.
    • (1995) Comput Appl Biosci , vol.11 , pp. 87-99
    • Sandak, B.1    Nussinov, R.2    Wolfson, H.J.3
  • 25
    • 84986492468 scopus 로고
    • Flexible ligand docking without parameter adjustment across four ligand-receptor complexes
    • Clark KP, Ajay: Flexible ligand docking without parameter adjustment across four ligand-receptor complexes. J Comput Chem 1995, 16:1210-1226.
    • (1995) J Comput Chem , vol.16 , pp. 1210-1226
    • Clark, K.P.1    Ajay2
  • 27
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones G, Willet P, Glen RC: Molecular 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    Willet, P.2    Glen, R.C.3
  • 28
  • 29
    • 0027216905 scopus 로고
    • The joys and vicissitudes of protein science
    • Koshland DE Jr: The joys and vicissitudes of protein science. Protein Sci 1993, 2:1364-1368.
    • (1993) Protein Sci , vol.2 , pp. 1364-1368
    • Koshland D.E., Jr.1
  • 30
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach AR: Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 1994, 235:345-356.
    • (1994) J Mol Biol , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 31
    • 0028291376 scopus 로고
    • Molecular dynamics simulation of the docking of substrates to proteins
    • Di Nola A, Roccatano D, Berendsen HJC: Molecular dynamics simulation of the docking of substrates to proteins. Proteins 1994, 19:174-182.
    • (1994) Proteins , vol.19 , pp. 174-182
    • Di Nola, A.1    Roccatano, D.2    Berendsen, H.J.C.3
  • 33
    • 0029450365 scopus 로고
    • Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions
    • Poornima CS, Dean PM: Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J Comput Aided Mol Des 1995, 9:500-512.
    • (1995) J Comput Aided Mol des , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 34
    • 0028047009 scopus 로고
    • Rational drug design: The proteinase inhibitors
    • Wlodawer A: Rational drug design: the proteinase inhibitors. Pharmacotherapy 1994, 14(suppl2):9-20.
    • (1994) Pharmacotherapy , vol.14 , Issue.12 SUPPL. , pp. 9-20
    • Wlodawer, A.1
  • 36
    • 0028181137 scopus 로고
    • Monte Carlo docking of protein-DNA complexes: Incorporation of DNA flexibility and experimental data
    • Knetgel RMA, Boelens R, Kaptein R: Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data. Protein Eng 1994, 7:761-767.
    • (1994) Protein Eng , vol.7 , pp. 761-767
    • Knetgel, R.M.A.1    Boelens, R.2    Kaptein, R.3
  • 41
    • 0028493139 scopus 로고
    • Current methods for site-directed structure generation
    • Lewis RA, Leach A: Current methods for site-directed structure generation. J Comput Aided Mol Des 1994, 8:467-475.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 467-475
    • Lewis, R.A.1    Leach, A.2
  • 42
    • 0028584446 scopus 로고
    • Structure-based drug design
    • Colman PM: Structure-based drug design. Curr Opin Struct Biol 1994, 4:868-874.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 868-874
    • Colman, P.M.1
  • 43
    • 0027942499 scopus 로고
    • Software for structure-based drug design
    • Guida WC: Software for structure-based drug design. Curr Opin Struct Biol 1994, 4:777-781.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 777-781
    • Guida, W.C.1
  • 45
    • 0343445468 scopus 로고
    • Combinatorial Libraries: The Theory and Practice of Combinatorial Chemistry
    • Leiden: ESCOM Science Publishers BV
    • Houghton RA: Combinatorial Libraries: the Theory and Practice of Combinatorial Chemistry. Perspectives in Drug Discovery and Design. Leiden: ESCOM Science Publishers BV; 1995.
    • (1995) Perspectives in Drug Discovery and Design
    • Houghton, R.A.1
  • 46
    • 0026649231 scopus 로고
    • Directed evolution of an RNA enzyme
    • Beaudry AA, Joyce GF: Directed evolution of an RNA enzyme. Science 1992, 257:635-641.
    • (1992) Science , vol.257 , pp. 635-641
    • Beaudry, A.A.1    Joyce, G.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.