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Volumn 9, Issue 1, 2008, Pages 65-77

Computational study for protein-protein docking using global optimization and empirical potentials

Author keywords

Combined CSA SA; Conformational space annealing; FastContact; Global optimization; Protein protein docking; Simulated annealing

Indexed keywords

ALGORITHM; ARTICLE; CALCULATION; CRYSTAL STRUCTURE; ENERGY; MOLECULAR DOCKING; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

EID: 39349094382     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms9010065     Document Type: Article
Times cited : (14)

References (37)
  • 2
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • DOI 10.1073/pnas.93.1.13
    • Jones, S.; Thornton, J.M. Principles of protein-protein interactions. Proc. Natl. Acad. Sci. USA. 1996, 93, 13-20; DOI 10.1073/pnas.93.1.13.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 3
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • DOI 10.1016/S0959-440X(02)00285-3;
    • Smith, G.R.; Sternberg, M.J.E. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct. Biol. 2002, 12, 28-35; DOI 10.1016/S0959-440X(02)00285-3;
    • (2002) Curr. Opin. Struct. Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 4
    • 0035281357 scopus 로고    scopus 로고
    • Computer simulation of protein-protein interactions
    • DOI 10.1021/jp003602d
    • Elcock, A.H.; Sept, D.; McCammon, J.A. Computer simulation of protein-protein interactions. J. Phys. Chem. B 2001, 105, 1504-1518; DOI 10.1021/jp003602d.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 1504-1518
    • Elcock, A.H.1    Sept, D.2    McCammon, J.A.3
  • 5
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • DOI 10.1016/j.sbi.2006.02.002;
    • Bonvin, A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 194-200; DOI 10.1016/j.sbi.2006.02.002;
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 6
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • DOI 10.1016/j.sbi.2006.03. 003;
    • Gary, J.J. High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 183-193; DOI 10.1016/j.sbi.2006.03. 003;
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 183-193
    • Gary, J.J.1
  • 7
    • 0032054715 scopus 로고    scopus 로고
    • Predictive docking of protein-protein and protein-DNA complexes
    • DOI 10.1016/S0959-440X(98)80047-X;
    • Sternberg, M.J.E.; Gabb, H.A.; Jackson, R.M. Predictive docking of protein-protein and protein-DNA complexes. Curr. Opin. Struct. Biol. 1998, 8, 250-256; DOI 10.1016/S0959-440X(98)80047-X;
    • (1998) Curr. Opin. Struct. Biol , vol.8 , pp. 250-256
    • Sternberg, M.J.E.1    Gabb, H.A.2    Jackson, R.M.3
  • 8
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • DOI 10.1002/prot.10115;
    • Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002, 47, 409-443; DOI 10.1002/prot.10115;
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 10
    • 0028984540 scopus 로고
    • Protein docking for low-resolution structures
    • DOI 10.1093/protein/8.4.371;
    • Vakser, I.A. Protein docking for low-resolution structures. Protein Eng. 1995, 8, 371-377; DOI 10.1093/protein/8.4.371;
    • (1995) Protein Eng , vol.8 , pp. 371-377
    • Vakser, I.A.1
  • 11
    • 0031565730 scopus 로고    scopus 로고
    • Modeling protein docking using shape complementarity, electrostatics and biochemical information
    • DOI 10.1006/jmbi.1997.1203;
    • Gabb, H.A.; Jackson, R.M.; Sternberg, M.J.E. Modeling protein docking using shape complementarity, electrostatics and biochemical information. J. Mol. Biol. 1997, 272, 106-120; DOI 10.1006/jmbi.1997.1203;
    • (1997) J. Mol. Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 12
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity desolvation, and electrostatics
    • DOI 10.1002/prot.10092;
    • Chen, R.; Weng, Z. Docking unbound proteins using shape complementarity desolvation, and electrostatics. Proteins 2002, 47, 281-294; DOI 10.1002/prot.10092;
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 14
    • 0028066542 scopus 로고
    • The Fourier-Greens function and the rapid evaluation of molecular potentials
    • DOI 10.1093/protein/7.3.359;
    • Harrison, R.W.; Kourinov, I.V.; Andrews, L.C. The Fourier-Greens function and the rapid evaluation of molecular potentials. Protein Eng. 1994, 7, 359-369; DOI 10.1093/protein/7.3.359;
    • (1994) Protein Eng , vol.7 , pp. 359-369
    • Harrison, R.W.1    Kourinov, I.V.2    Andrews, L.C.3
  • 16
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S.; Gelatt, C.D.; Vecchi, M.P. Optimization by simulated annealing. Science 1983, 220, 671-680;
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 17
    • 0029058162 scopus 로고
    • Side-chain prediction by neural networks and simulated annealing optimization
    • DOI 10.1093/protein/8.4.363;
    • Hwang, J.; Liao, W. Side-chain prediction by neural networks and simulated annealing optimization. Protein Eng. 1995, 8, 363-370; DOI 10.1093/protein/8.4.363;
    • (1995) Protein Eng , vol.8 , pp. 363-370
    • Hwang, J.1    Liao, W.2
  • 18
    • 0021819411 scopus 로고
    • Thermodynamical approach to the traveling salesman problem: An efficient simulation algorithm
    • DOI 10.1007/BF00940812
    • Cerny, V. Thermodynamical approach to the traveling salesman problem: an efficient simulation algorithm. J. Optim. Theory Appl. 1985, 45, 41-51; DOI 10.1007/BF00940812.
    • (1985) J. Optim. Theory Appl , vol.45 , pp. 41-51
    • Cerny, V.1
  • 19
    • 17644434733 scopus 로고    scopus 로고
    • Placement by thermodynamic simulated annealing
    • DOI 10.1016/j.physleta.2003.08.070
    • de Vicente, J.; Lanchares, J.; Hermida, R. Placement by thermodynamic simulated annealing. Phys. Lett. A 2003, 317, 415-423; DOI 10.1016/j.physleta.2003.08.070.
    • (2003) Phys. Lett. A , vol.317 , pp. 415-423
    • de Vicente, J.1    Lanchares, J.2    Hermida, R.3
  • 20
    • 0001176785 scopus 로고    scopus 로고
    • Lee, J.; Scheraga, H.A.; Rackovsky, S. New optimization method for conformational energy calculations on polypeptide: conformational space annealing. J. Comput. Chem. 1997, 18, 1222-1232; DOI 10.1002/(SICI)1096-987X(19970715)18:9〈1222::AID-JCC10〉3.0.CO;2-7.
    • Lee, J.; Scheraga, H.A.; Rackovsky, S. New optimization method for conformational energy calculations on polypeptide: conformational space annealing. J. Comput. Chem. 1997, 18, 1222-1232; DOI 10.1002/(SICI)1096-987X(19970715)18:9〈1222::AID-JCC10〉3.0.CO;2-7.
  • 21
    • 11144254064 scopus 로고    scopus 로고
    • An efficient molecular docking using conformational space annealing
    • Lee, K.; Czaplewski, C.; Kim, S.-Y.; Lee, J. An efficient molecular docking using conformational space annealing. J. Comput. Chem. 2005, 26, 78-87;
    • (2005) J. Comput. Chem , vol.26 , pp. 78-87
    • Lee, K.1    Czaplewski, C.2    Kim, S.-Y.3    Lee, J.4
  • 22
    • 21644432715 scopus 로고    scopus 로고
    • Study of protein-protein interaction using conformational space annealing
    • DOI 10.1002/prot.20567;
    • Lee, K.; Sim, J.; Lee, J. Study of protein-protein interaction using conformational space annealing. Proteins 2005, 60, 257-262; DOI 10.1002/prot.20567;
    • (2005) Proteins , vol.60 , pp. 257-262
    • Lee, K.1    Sim, J.2    Lee, J.3
  • 23
    • 0038359614 scopus 로고    scopus 로고
    • Janin, J.; Hendrick, K.; Moult, J.; Eyck, L.T.; Sternberg, M.J.E.; Vajda, S.; Vakser, I.A.; Wodak, S.J. CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 2003, 52, 2-9; DOI 10.1002/prot.10381;
    • Janin, J.; Hendrick, K.; Moult, J.; Eyck, L.T.; Sternberg, M.J.E.; Vajda, S.; Vakser, I.A.; Wodak, S.J. CAPRI: A Critical Assessment of PRedicted Interactions. Proteins 2003, 52, 2-9; DOI 10.1002/prot.10381;
  • 24
    • 18844462557 scopus 로고    scopus 로고
    • FastContact: Rapid estimate of contact and binding free energies
    • DOI 10.1093/bioinformatics/bti322;
    • Camacho, C.J.; Zhang, C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005, 21, 2534-2536; DOI 10.1093/bioinformatics/bti322;
    • (2005) Bioinformatics , vol.21 , pp. 2534-2536
    • Camacho, C.J.1    Zhang, C.2
  • 25
    • 34547572513 scopus 로고    scopus 로고
    • Champ, P.C.; Camacho, C.J. FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Research 2007, 35, W556-W560;
    • Champ, P.C.; Camacho, C.J. FastContact: a free energy scoring tool for protein-protein complex structures. Nucleic Acids Research 2007, 35, W556-W560;
  • 26
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack, R.L; Cohen, F.E. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci. 1997, 6, 1661-1681;
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack, R.L.1    Cohen, F.E.2
  • 29
    • 0000545402 scopus 로고
    • A comparative study of the simulated annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [met]-enkephalin
    • DOI 10.1002/jcc.540120509
    • Nayeem, A.; Vila, J.; Scheraga, H.A. A comparative study of the simulated annealing and Monte Carlo-with-minimization approaches to the minimum-energy structures of polypeptides: [met]-enkephalin. J. Comput. Chem. 1991, 12, 594-605; DOI 10.1002/jcc.540120509.
    • (1991) J. Comput. Chem , vol.12 , pp. 594-605
    • Nayeem, A.1    Vila, J.2    Scheraga, H.A.3
  • 30
    • 0032605909 scopus 로고    scopus 로고
    • Lee, J.; Liwo, A.; Ripoll, D.R.; Pillardy, J.; Scheraga, H.A. Calculation of protein conformation by global optimization of a potential energy function. Proteins Suppl. 1999, 3, 204-208; DOI 10.1002/(SICI)1097- 0134(1999)37:3+〈204::AID-PROT26〉3.0.CO;2-F.
    • Lee, J.; Liwo, A.; Ripoll, D.R.; Pillardy, J.; Scheraga, H.A. Calculation of protein conformation by global optimization of a potential energy function. Proteins Suppl. 1999, 3, 204-208; DOI 10.1002/(SICI)1097- 0134(1999)37:3+〈204::AID-PROT26〉3.0.CO;2-F.
  • 31
    • 4043058565 scopus 로고    scopus 로고
    • Prediction of protein tertiary structure using profesy, a novel method based on fragment assembly and conformational space annealing
    • Lee, J.; Kim, S-Y.; Joo, K.; Kim, I.; Lee, J. Prediction of protein tertiary structure using profesy, a novel method based on fragment assembly and conformational space annealing. Proteins 2004, 56, 704-714;
    • (2004) Proteins , vol.56 , pp. 704-714
    • Lee, J.1    Kim, S.-Y.2    Joo, K.3    Kim, I.4    Lee, J.5
  • 32
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations
    • DOI 10.1002/jcc.540040211
    • Brooks, B.R.; Bruccoleri, R.E.; Olafson, B.D.; States, D.J.; Karplus, M. CHARMM: a program for macromolecular energy, minimization, and molecular dynamics calculations J. Comput. Chem. 1983, 4, 187-217; DOI 10.1002/jcc.540040211.
    • (1983) J. Comput. Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1    Bruccoleri, R.E.2    Olafson, B.D.3    States, D.J.4    Karplus, M.5
  • 33
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • DOI 10.1021/ma00145a039
    • Miyazawa, S.; Jernigan, R. L. Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 1985, 18, 534-552; DOI 10.1021/ma00145a039.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 34
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • DOI 10.1006/jmbi.1996.0114;
    • Miyazawa, S.; Jernigan, R. L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996, 256, 623-644; DOI 10.1006/jmbi.1996.0114;
    • (1996) J. Mol. Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 35
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez, R.; Leplae, R.; de Maria, L.; Wodak, S. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003, 52, 51-67;
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    de Maria, L.3    Wodak, S.4
  • 36
    • 0032824805 scopus 로고    scopus 로고
    • Folding funnels and binding mechanisms
    • Ma, B.; Kumar, S.; Tsai, C.J.; Nussinov, R. Folding funnels and binding mechanisms. Protein Eng. 1999, 12, 713-720;
    • (1999) Protein Eng , vol.12 , pp. 713-720
    • Ma, B.1    Kumar, S.2    Tsai, C.J.3    Nussinov, R.4
  • 37
    • 0034916879 scopus 로고    scopus 로고
    • How common is the funnel-like energy landscape in protein-protein interactions
    • Tovchigrechko, A.; Vakser, I.A. How common is the funnel-like energy landscape in protein-protein interactions. Protein Science 2001, 10, 1572-1583;
    • (2001) Protein Science , vol.10 , pp. 1572-1583
    • Tovchigrechko, A.1    Vakser, I.A.2


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