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Volumn 39, Issue 4, 2000, Pages 372-384

Bigger: A new (soft) docking algorithm for predicting protein interactions

Author keywords

Algorithms; Macromolecular interactions; Molecular recognition; Molecular surface; Protein complexes; Protein docking; Protein interactions

Indexed keywords

ALGORITHM; ARTICLE; COMPLEX FORMATION; ENERGY; GEOMETRY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; X RAY CRYSTALLOGRAPHY;

EID: 0034212826     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.0.CO;2-Q     Document Type: Article
Times cited : (266)

References (35)
  • 1
    • 0026310932 scopus 로고
    • "Soft docking": Matching of molecular surface cubes
    • Jiang F, Kim SH. "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.H.2
  • 2
    • 0025785057 scopus 로고
    • Protein docking and complementarity
    • Shoichet BK, Kuntz ID. Protein docking and complementarity. J Mol Biol 1991;221:327-346.
    • (1991) J Mol Biol , vol.221 , pp. 327-346
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 3
    • 0026319198 scopus 로고
    • Protein-protein recognition analyzed by docking simulation
    • Cherfils J, Duquerroy S, Janin J. Protein-protein recognition analyzed by docking simulation. Proteins 1991;11:271-280.
    • (1991) Proteins , vol.11 , pp. 271-280
    • Cherfils, J.1    Duquerroy, S.2    Janin, J.3
  • 4
    • 0026642968 scopus 로고
    • Docking by least-squares fitting of molecular surface patterns
    • Bacon DJ, Moult J. Docking by least-squares fitting of molecular surface patterns. J Mol Biol 1992;225:849-858.
    • (1992) J Mol Biol , vol.225 , pp. 849-858
    • Bacon, D.J.1    Moult, J.2
  • 5
    • 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
  • 6
    • 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
  • 7
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 8
    • 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
  • 9
    • 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
  • 10
    • 0026464639 scopus 로고
    • New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking
    • Walls PH, Sternberg MJ. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol 1992;228:277-297.
    • (1992) J Mol Biol , vol.228 , pp. 277-297
    • Walls, P.H.1    Sternberg, M.J.2
  • 11
    • 0025912338 scopus 로고
    • Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors
    • Hubbard SJ, Campbell SF, Thornton JM. Molecular recognition. Conformational analysis of limited proteolytic sites and serine proteinase protein inhibitors. J Mol Biol 1991;220:507-530.
    • (1991) J Mol Biol , vol.220 , pp. 507-530
    • Hubbard, S.J.1    Campbell, S.F.2    Thornton, J.M.3
  • 12
    • 0027976930 scopus 로고
    • Molecular surface representations by sparse critical points
    • Lin SL, Nussinov R, Fischer D, Wolfson HJ. Molecular surface representations by sparse critical points. Proteins 1994;18:94-101.
    • (1994) Proteins , vol.18 , pp. 94-101
    • Lin, S.L.1    Nussinov, R.2    Fischer, D.3    Wolfson, H.J.4
  • 13
    • 0028079323 scopus 로고
    • Molecular surface recognition by a computer vision-based technique
    • Norel R, Fischer D, Wolfson HJ, Nussinov R. Molecular surface recognition by a computer vision-based technique. Protein Eng 1994;7:39-46.
    • (1994) Protein Eng , vol.7 , pp. 39-46
    • Norel, R.1    Fischer, D.2    Wolfson, H.J.3    Nussinov, R.4
  • 14
    • 0028166881 scopus 로고
    • Shape complementarity at protein-protein interfaces
    • Norel R, Lin SL, Wolfson HJ, Nussinov R. Shape complementarity at protein-protein interfaces. Biopolymers 1994;34:933-940.
    • (1994) Biopolymers , vol.34 , pp. 933-940
    • Norel, R.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 15
    • 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 HJ, 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.J.3    Nussinov, R.4
  • 16
    • 0030855390 scopus 로고    scopus 로고
    • ESCHER: A new docking procedure applied to the reconstruction of protein tertiary structure
    • Ausiello G, Cesareni G, Helmer-Citterich M. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins 1997;28:556-567.
    • (1997) Proteins , vol.28 , pp. 556-567
    • Ausiello, G.1    Cesareni, G.2    Helmer-Citterich, M.3
  • 17
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997;272:106-120.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.3
  • 19
    • 0028455325 scopus 로고
    • Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
    • Meng EC, Kuntz ID, Abraham DJ, Kellogg GE. Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities. J Comput Aided Mol Des 1994;8:299-306.
    • (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
  • 20
    • 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
  • 21
    • 0030598347 scopus 로고    scopus 로고
    • Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking
    • Meyer M, Wilson P, Schomburg D. Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol 1996;264:199-210.
    • (1996) J Mol Biol , vol.264 , pp. 199-210
    • Meyer, M.1    Wilson, P.2    Schomburg, D.3
  • 22
    • 0029940017 scopus 로고    scopus 로고
    • Empirical free energy as a target function in docking and design: Application to HIV-1 protease inhibitors
    • King BL, Vajda S, DeLisi C. Empirical free energy as a target function in docking and design: application to HIV-1 protease inhibitors. FEBS Lett 1996;384:87-91.
    • (1996) FEBS Lett , vol.384 , pp. 87-91
    • King, B.L.1    Vajda, S.2    DeLisi, C.3
  • 23
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Application to the docking problem
    • Jackson RM, Sternberg MJ. A continuum model for protein-protein interactions: application to the docking problem. J Mol Biol 1995;250:258-275.
    • (1995) J Mol Biol , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, M.J.2
  • 27
    • 0011134241 scopus 로고    scopus 로고
    • Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions
    • Halgren TA. Merck Molecular Force Field. II. MMFF94 van der Waals and Electrostatic Parameters for Intermolecular Interactions. J Comp Chem 1996;17:520-552.
    • (1996) J Comp Chem , vol.17 , pp. 520-552
    • Halgren, T.A.1
  • 28
    • 0029077858 scopus 로고
    • A new computational model for protein folding based on atomic solvation
    • Wang Y, Zhang H, Scott RA. A new computational model for protein folding based on atomic solvation. Protein Sci 1995;4:1402-1411.
    • (1995) Protein Sci , vol.4 , pp. 1402-1411
    • Wang, Y.1    Zhang, H.2    Scott, R.A.3
  • 29
    • 0028895567 scopus 로고
    • Discriminating compact nonnative structures from the native structure of globular proteins
    • Wang Y, Zhang H, Li W, Scott RA. Discriminating compact nonnative structures from the native structure of globular proteins. Proc Natl Acad Sci USA 1995;92:709-713.
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 709-713
    • Wang, Y.1    Zhang, H.2    Li, W.3    Scott, R.A.4
  • 30
    • 0022471098 scopus 로고
    • Learning representations of back-propagation errors
    • Rumelhart DE, Hinton GE, Williams RJ. Learning representations of back-propagation errors. Nature 1986;323:533-536.
    • (1986) Nature , vol.323 , pp. 533-536
    • Rumelhart, D.E.1    Hinton, G.E.2    Williams, R.J.3
  • 33


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.