메뉴 건너뛰기




Volumn , Issue , 2005, Pages 159-173

Using residue propensities and tightness of fit to improve rigid-body protein-protein docking

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY-ANTIGEN; BENCHMARK DATA; BIOLOGICAL FUNCTIONS; COMPUTATIONAL APPROACH; ENZYME-INHIBITOR COMPLEX; PHYSIO-CHEMICAL PROPERTIES; PROTEIN INTERACTION; PROTEIN-PROTEIN DOCKING; PROTEIN-PROTEIN INTERACTIONS; RIGID BODY; RIGID-BODY DOCKING; SCORING FUNCTIONS; SHAPE COMPLEMENTARITY;

EID: 34548751574     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (6)

References (35)
  • 3
    • 17444372787 scopus 로고    scopus 로고
    • Improved prediction of protein-protein binding sites using a support vector machines approach
    • James Bradford and David Westhead. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics, 21(8):1487-1494, 2005.
    • (2005) Bioinformatics , vol.21 , Issue.8 , pp. 1487-1494
    • Bradford, J.1    Westhead, D.2
  • 5
    • 0038187616 scopus 로고    scopus 로고
    • Weighted geometric docking: Incorporating external information in the rotation-translation scan
    • Efrat Ben-Zeev and Miriam Eisenstein. Weighted geometric docking: Incorporating External Information in the Rotation-Translation Scan. Proteins: Structure, Function and Genetics, 52:24-27, 2003.
    • (2003) Proteins: Structure, Function and Genetics , vol.52 , pp. 24-27
    • Ben-Zeev, E.1    Eisenstein, M.2
  • 6
    • 0345832301 scopus 로고    scopus 로고
    • Cluspro: An automated docking and discrimination method for the prediction of protein complexes
    • S.R. Comeau, D.W. Gatchell, S. Vajda, and C.J. Camacho. ClusPro: an automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20:45-50, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 8
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarirty scoring function for protein-protein docking
    • R Chen and Z Weng. A Novel Shape Complementarirty Scoring Function for Protein-Protein Docking. Proteins, 51:397-408, 2003.
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 9
    • 3543090867 scopus 로고    scopus 로고
    • Using convex hulls to extract interaction interfaces from known structures
    • Panos Dafas, Dan Bolser, Jacek Gomoluch, Jong Park, and Michael Schroeder. Using convex hulls to extract interaction interfaces from known structures. Bioinformatics, 20(10):1486-1490, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1486-1490
    • Dafas, P.1    Bolser, D.2    Gomoluch, J.3    Park, J.4    Schroeder, M.5
  • 10
    • 13244277453 scopus 로고    scopus 로고
    • Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions
    • Y. Duan, V.B. Reddy, and YN. Kaznessis. Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions. Protein Science, 14:316-328, 2005.
    • (2005) Protein Science , vol.14 , pp. 316-328
    • Duan, Y.1    Reddy, V.B.2    Kaznessis, Y.N.3
  • 12
    • 2942589060 scopus 로고    scopus 로고
    • On proteins, grids, correlations, and docking
    • M. Eisenstein and E. Katchalski-Katzir. On proteins, grids, correlations, and docking. C.R.Biologies, 327:409-420, 2004.
    • (2004) C.R.Biologies , vol.327 , pp. 409-420
    • Eisenstein, M.1    Katchalski-Katzir, E.2
  • 13
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complimentarity, electrostatics and biochemical information
    • H. Gabb, R. Jackson, and M. Sternberg. Modelling Protein Docking using Shape Complimentarity, Electrostatics and Biochemical Information. J.Mol.Biol, 272(1):106-120, 1997.
    • (1997) J.Mol.Biol , vol.272 , Issue.1 , pp. 106-120
    • Gabb, H.1    Jackson, R.2    Sternberg, M.3
  • 14
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, and D Baker. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol., 331:281-299, 2003.
    • (2003) J. Mol. Biol. , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 15
    • 1842595135 scopus 로고    scopus 로고
    • A novel method for scoring of docked protein complexes using predicted protein-protein binding sites
    • K.E. Gottschalk, H Neuvirth, and G. Schreiber. A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng. Des., 17:183-189, 2004.
    • (2004) Protein Eng. Des. , vol.17 , pp. 183-189
    • Gottschalk, K.E.1    Neuvirth, H.2    Schreiber, G.3
  • 16
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • G. Moont H.A. Gabb and M.J. Sternberg. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins, 35(3):364-373, 1999.
    • (1999) Proteins , vol.35 , Issue.3 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 17
    • 0035342450 scopus 로고    scopus 로고
    • Residue frequencies and pairing preferences at protein-protein interfaces
    • F. Glaser, DM. Steinberg, IA. Vakser, and N. Ben-Tal. Residue Frequencies and Pairing Preferences at Protein-Protein Interfaces. Proteins, 43:82-102, 2001.
    • (2001) Proteins , vol.43 , pp. 82-102
    • Glaser, F.1    Steinberg, D.M.2    Vakser, I.A.3    Ben-Tal, N.4
  • 18
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • I Halperin, B Ma, H Wolfson, and R Nussinov. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins, 47:409-443, 2002.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 19
    • 0032981632 scopus 로고    scopus 로고
    • Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: Implications for the protein docking problem
    • RM Jackson. Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci, 8:603-613, 1999.
    • (1999) Protein Sci , vol.8 , pp. 603-613
    • Jackson, R.M.1
  • 20
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • Susan Jones and Janet Thornton. Analysis of protein-protein interaction sites using surface patches. J.Mol.Biol, 272:121-132, 1997.
    • (1997) J.Mol.Biol , vol.272 , pp. 121-132
    • Jones, S.1    Thornton, J.2
  • 21
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patches analysis
    • Susan Jones and Janet Thornton. Prediction of protein-protein interaction sites using patches analysis. J.Mol.Biol, 272:133-143, 1997.
    • (1997) J.Mol.Biol , vol.272 , pp. 133-143
    • Jones, S.1    Thornton, J.2
  • 22
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • J.Recio, M Totrov, and R Abagyan. Soft protein-protein docking in internal coordinates. Protein Sci, 11:280-291, 2002.
    • (2002) Protein Sci , vol.11 , pp. 280-291
    • Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 24
    • 0033665510 scopus 로고    scopus 로고
    • Ball-Rapid software prototyping in computational molecular biology
    • O. Kohlbacher and H.P. Lenhof. BALL-Rapid Software Prototyping in Computational Molecular Biology. Bioinformatics, 16(9):815-824, 2000.
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 815-824
    • Kohlbacher, O.1    Lenhof, H.P.2
  • 25
    • 0242299200 scopus 로고    scopus 로고
    • Rdock: Refinement of rigid-body protein docking predictions
    • L Li, R Chen, and W Zhiping. RDOCK: refinement of rigid-body protein docking predictions. Proteins, 53(3):693-707, 2003.
    • (2003) Proteins , vol.53 , Issue.3 , pp. 693-707
    • Li, L.1    Chen, R.2    Zhiping, W.3
  • 26
    • 0037846433 scopus 로고    scopus 로고
    • A protein-protein docking algorithm dependent on the type of complexes
    • ChunHua Li, XiaoHui Ma, WeiZu Chen, and CunXin Wan. A protein-protein docking algorithm dependent on the type of complexes. Protein Eng., 16:265-269, 2003.
    • (2003) Protein Eng. , vol.16 , pp. 265-269
    • Li, C.H.1    Ma, X.H.2    Chen, W.Z.3    Wan, C.X.4
  • 27
    • 1842526090 scopus 로고    scopus 로고
    • Promate: A structure based prediction program to indentify the location of protein-protein binding stes
    • Hani Neuvirth, Ran Raz, and Gibeon Schreiber. ProMate: A structure based prediction program to indentify the location of protein-protein binding stes. J.Mol.Biol, 338:181-199, 2004.
    • (2004) J.Mol.Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 28
    • 0034212826 scopus 로고    scopus 로고
    • Bigger: A new (soft) docking algorithm for predicting protein interactions
    • P.N. Palma, L Krippahl, J.E. Wampler, and J.G. Moura. BiGGER: A new (soft) docking algorithm for predicting protein interactions. Proteins, 39(4):372-384, 2000.
    • (2000) Proteins , vol.39 , Issue.4 , pp. 372-384
    • Palma, P.N.1    Krippahl, L.2    Wampler, J.E.3    Moura, J.G.4
  • 29
    • 0035970298 scopus 로고    scopus 로고
    • Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the pdb and yeast
    • J. Park, M. Lappe, and S.A. Teichmann. Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol, 307(3):929-38, 2001.
    • (2001) J Mol Biol , vol.307 , Issue.3 , pp. 929-938
    • Park, J.1    Lappe, M.2    Teichmann, S.A.3
  • 30
  • 31
    • 0032054715 scopus 로고    scopus 로고
    • Predictive docking of protein-protein and protein-dna complexes
    • MJ Sternberg, HA Gabb, and RM Jackson. Predictive docking of protein-protein and protein-DNA complexes. Curr. Opin. Struct Biol., 8(2):265-269, 1998.
    • (1998) Curr. Opin. Struct Biol. , vol.8 , Issue.2 , pp. 265-269
    • Sternberg, M.J.1    Gabb, H.A.2    Jackson, R.M.3
  • 32
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • GR Smith and MJ Sternberg. Prediction of protein-protein interactions by docking methods. Curr. Opin. Struct Biol., 12:28-35, 2002.
    • (2002) Curr. Opin. Struct Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 34
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: Is the glass half-full or half-empty?
    • S Vajda and CJ Camacho. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol., 22(3):110-116, 2004.
    • (2004) Trends Biotechnol. , vol.22 , Issue.3 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 35
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • HX Zhou and Y. Shan. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins: Structure, Function, and Genetics, 44(3):336-343, 2001.
    • (2001) Proteins: Structure, Function, and Genetics , vol.44 , Issue.3 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.