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Volumn 57, Issue 3, 2004, Pages 548-557

Prediction of the interaction site on the surface of an isolated protein structure by analysis of side chain energy scores

Author keywords

Binding free energy; Molecular recognition; Patch analysis; Protein protein interface; Side chain energy

Indexed keywords

HYDROGEN; MONOMER;

EID: 6344291590     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20238     Document Type: Article
Times cited : (13)

References (32)
  • 1
    • 0347089142 scopus 로고    scopus 로고
    • Effective scoring function for protein sequence design
    • Liang S, Grishin NV. Effective scoring function for protein sequence design. Proteins 2004;54(2):271-81.
    • (2004) Proteins , vol.54 , Issue.2 , pp. 271-281
    • Liang, S.1    Grishin, N.V.2
  • 2
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98(19):10636-41.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.19 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2
  • 3
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12(1):28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , Issue.1 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 4
    • 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(6):2195-9.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.6 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 5
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • Moont G, Gabb HA, Sternberg MJ. Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999;35(3):364-73.
    • (1999) Proteins , vol.35 , Issue.3 , pp. 364-373
    • Moont, G.1    Gabb, H.A.2    Sternberg, M.J.3
  • 6
    • 0034212826 scopus 로고    scopus 로고
    • BiGGER: A new (soft) docking algorithm for predicting protein interactions
    • Palma PN, Krippahl L, Wampler JE, Moura JJ. BiGGER: a new (soft) docking algorithm for predicting protein interactions. Proteins 2000;39(4):372-84.
    • (2000) Proteins , vol.39 , Issue.4 , pp. 372-384
    • Palma, P.N.1    Krippahl, L.2    Wampler, J.E.3    Moura, J.J.4
  • 7
    • 0034769223 scopus 로고    scopus 로고
    • Electrostatic contributions to protein-protein interactions: Fast energetic filters for docking and their physical basis
    • Norel R, Sheinerman F, Petrey D, Honig B. Electrostatic contributions to protein-protein interactions: fast energetic filters for docking and their physical basis. Protein Sci 2001;10(11):2147-61.
    • (2001) Protein Sci , vol.10 , Issue.11 , pp. 2147-2161
    • Norel, R.1    Sheinerman, F.2    Petrey, D.3    Honig, B.4
  • 8
    • 0035141353 scopus 로고    scopus 로고
    • Dynamical view of the positions of key side chains in protein-protein recognition
    • Kimura SR, Brower RC, Vajda S, Camacho CJ. Dynamical view of the positions of key side chains in protein-protein recognition. Biophys J 2001;80(2):635-42.
    • (2001) Biophys J , vol.80 , Issue.2 , pp. 635-642
    • Kimura, S.R.1    Brower, R.C.2    Vajda, S.3    Camacho, C.J.4
  • 9
    • 0031565729 scopus 로고    scopus 로고
    • Analysis of protein-protein interaction sites using surface patches
    • Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997;272(1):121-32.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 121-132
    • Jones, S.1    Thornton, J.M.2
  • 10
    • 0031565725 scopus 로고    scopus 로고
    • Prediction of protein-protein interaction sites using patch analysis
    • Jones S, Thornton JM. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol 1997;272(1):133-43.
    • (1997) J Mol Biol , vol.272 , Issue.1 , pp. 133-143
    • Jones, S.1    Thornton, J.M.2
  • 11
    • 0028332007 scopus 로고
    • A role for surface hydrophobicity in protein-protein recognition
    • Young L, Jernigan RL, Covell DG. A role for surface hydrophobicity in protein-protein recognition. Protein Sci 1994;3(5):717-29.
    • (1994) Protein Sci , vol.3 , Issue.5 , pp. 717-729
    • Young, L.1    Jernigan, R.L.2    Covell, D.G.3
  • 12
    • 1842405464 scopus 로고    scopus 로고
    • Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect
    • Tsai CJ, Lin SL, Wolfson HJ, Nussinov R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect. Protein Sci 1997;6(1):53-64.
    • (1997) Protein Sci , vol.6 , Issue.1 , pp. 53-64
    • Tsai, C.J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 13
    • 0030028728 scopus 로고    scopus 로고
    • Principles of protein-protein interactions
    • Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996;93(1):13-20.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.1 , pp. 13-20
    • Jones, S.1    Thornton, J.M.2
  • 14
    • 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(5):2177-98.
    • (1999) J Mol Biol , vol.285 , Issue.5 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 15
    • 0036893020 scopus 로고    scopus 로고
    • Side-chain conformational entropy at protein-protein interfaces
    • Cole C, Warwicker J. Side-chain conformational entropy at protein-protein interfaces. Protein Sci 2002;11(12):2860-70.
    • (2002) Protein Sci , vol.11 , Issue.12 , pp. 2860-2870
    • Cole, C.1    Warwicker, J.2
  • 16
    • 0037422589 scopus 로고    scopus 로고
    • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions
    • Fernandez A, Scheraga HA. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc Natl Acad Sci USA 2003;100(1):113-8.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.1 , pp. 113-118
    • Fernandez, A.1    Scheraga, H.A.2
  • 17
    • 0031450506 scopus 로고    scopus 로고
    • Hydrogen bonds and salt bridges across protein-protein interfaces
    • Xu D, Tsai CJ, Nussinov R. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng 1997;10(9):999-1012.
    • (1997) Protein Eng , vol.10 , Issue.9 , pp. 999-1012
    • Xu, D.1    Tsai, C.J.2    Nussinov, R.3
  • 18
    • 0029584688 scopus 로고
    • What makes a binding site a binding site?
    • Ringe D. What makes a binding site a binding site? Curr Opin Struct Biol 1995;5(6):825-9.
    • (1995) Curr Opin Struct Biol , vol.5 , Issue.6 , pp. 825-829
    • Ringe, D.1
  • 20
    • 0033614004 scopus 로고    scopus 로고
    • Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
    • Word JM, Lovell SC, Richardson JS, Richardson DC. Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation. J Mol Biol 1999;285(4):1735-47.
    • (1999) J Mol Biol , vol.285 , Issue.4 , pp. 1735-1747
    • Word, J.M.1    Lovell, S.C.2    Richardson, J.S.3    Richardson, D.C.4
  • 21
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack RL, Jr., Cohen FE. Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci 1997;6(8):1661-81.
    • (1997) Protein Sci , vol.6 , Issue.8 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 22
    • 0027971497 scopus 로고
    • Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1
    • Braden BC, Souchon H, Eisele JL, Bentley GA, Bhat TN, Navaza J, Poljak RJ. Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J Mol Biol 1994;243(4):767-81.
    • (1994) J Mol Biol , vol.243 , Issue.4 , pp. 767-781
    • Braden, B.C.1    Souchon, H.2    Eisele, J.L.3    Bentley, G.A.4    Bhat, T.N.5    Navaza, J.6    Poljak, R.J.7
  • 23
    • 0029056922 scopus 로고
    • Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles
    • Schreiber G, Fersht AR. Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles. J Mol Biol 1995;248(2):478-86.
    • (1995) J Mol Biol , vol.248 , Issue.2 , pp. 478-486
    • Schreiber, G.1    Fersht, A.R.2
  • 24
    • 0029766569 scopus 로고    scopus 로고
    • Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor: Effects on the kinetics and thermodynamics of binding to beta-trypsin and alpha-chymotrypsin
    • Castro MJ, Anderson S. Alanine point-mutations in the reactive region of bovine pancreatic trypsin inhibitor: effects on the kinetics and thermodynamics of binding to beta-trypsin and alpha-chymotrypsin. Biochemistry 1996;35(35):11435-46.
    • (1996) Biochemistry , vol.35 , Issue.35 , pp. 11435-11446
    • Castro, M.J.1    Anderson, S.2
  • 27
    • 0037007068 scopus 로고    scopus 로고
    • Computational mapping identifies the binding sites of organic solvents on proteins
    • Dennis S, Kortvelyesi T, Vajda S. Computational mapping identifies the binding sites of organic solvents on proteins. Proc Natl Acad Sci USA 2002;99(7):4290-5.
    • (2002) Proc Natl Acad Sci USA , vol.99 , Issue.7 , pp. 4290-4295
    • Dennis, S.1    Kortvelyesi, T.2    Vajda, S.3
  • 29
    • 0042386537 scopus 로고    scopus 로고
    • Identification of substrate binding sites in enzymes by computational solvent mapping
    • Silberstein M, Dennis S, Brown L, Kortvelyesi T, Clodfelter K, Vajda S. Identification of substrate binding sites in enzymes by computational solvent mapping. J Mol Biol 2003;332(5):1095-113.
    • (2003) J Mol Biol , vol.332 , Issue.5 , pp. 1095-1113
    • Silberstein, M.1    Dennis, S.2    Brown, L.3    Kortvelyesi, T.4    Clodfelter, K.5    Vajda, S.6
  • 30
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci 1998;7(9):1884-97.
    • (1998) Protein Sci , vol.7 , Issue.9 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 31
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • Brady GP, Jr., Stouten PF. Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided Mol Des 2000;14(4):383-401.
    • (2000) J Comput Aided Mol des , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.2
  • 32
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen MJ, Clifton JG, Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc Natl Acad Sci USA 2001;98(22):12473-8.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.22 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.