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Volumn 9, Issue 4, 2000, Pages 765-775

Analysis of knowledge-based protein-ligand potentials using a self- consistent method

Author keywords

Computational ligand design; Knowledge based potentials; Protein ligand interactions; Self consistent method

Indexed keywords

LIGAND; PROTEIN;

EID: 0034092711     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.9.4.765     Document Type: Article
Times cited : (30)

References (37)
  • 1
    • 0029623184 scopus 로고
    • Computational methods to predict binding free energy in ligand-receptor complexes
    • Ajay, Murcko MA. 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 38:4953-4967.
    • (1995) J Med Chem , vol.38 , pp. 4953-4967
    • Ajay1    Murcko, M.A.2
  • 2
    • 0031189711 scopus 로고    scopus 로고
    • Molecular recognition of protein-ligand complexes: Applications to drug design
    • Babine RE, Bender SL. 1997. Molecular recognition of protein-ligand complexes: Applications to drug design. Chem Rev 97:1359-1472.
    • (1997) Chem Rev , vol.97 , pp. 1359-1472
    • Babine, R.E.1    Bender, S.L.2
  • 4
    • 0033005899 scopus 로고    scopus 로고
    • Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
    • Betancourt MR, Thirumalai D. 1999. Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci 8:361-369.
    • (1999) Protein Sci , vol.8 , pp. 361-369
    • Betancourt, M.R.1    Thirumalai, D.2
  • 6
    • 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 H. 1994. 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 8:243-256.
    • (1994) J Comput-Aided Mol Des , vol.8 , pp. 243-256
    • Böhm, H.1
  • 7
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • Böhm H. 1998. Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J Comput-Aided Mol Des 12:309-323.
    • (1998) J Comput-Aided Mol Des , vol.12 , pp. 309-323
    • Böhm, H.1
  • 10
    • 0031003647 scopus 로고    scopus 로고
    • SMoG: De novo design method based on simple, fast and accurate free energy estimates. 2. Case studies in molecular design
    • DeWitte RS, Ishchenko AV, Shakhnovich EI. 1997. SMoG: De novo design method based on simple, fast and accurate free energy estimates. 2. Case studies in molecular design. J Am Chem Soc 119:4608-4617.
    • (1997) J Am Chem Soc , vol.119 , pp. 4608-4617
    • DeWitte, R.S.1    Ishchenko, A.V.2    Shakhnovich, E.I.3
  • 11
    • 0028072364 scopus 로고
    • Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy
    • DeWitte RS, Shakhnovich EI. 1994. Pseudodihedrals: Simplified protein backbone representation with knowledge-based energy. Protein Sci 3:1570-1581.
    • (1994) Protein Sci , vol.3 , pp. 1570-1581
    • DeWitte, R.S.1    Shakhnovich, E.I.2
  • 12
    • 0000934205 scopus 로고    scopus 로고
    • SMoG: De novo design method based on simple, fast and accurate free energy estimates. 1. Methodology and supporting evidence
    • DeWitte RS, Shakhnovich EI. 1996. SMoG: De novo design method based on simple, fast and accurate free energy estimates. 1. Methodology and supporting evidence. J Am Chem Soc 118: 11733-11744.
    • (1996) J Am Chem Soc , vol.118 , pp. 11733-11744
    • DeWitte, R.S.1    Shakhnovich, E.I.2
  • 13
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. 1997. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput-Aided Mol Des 11:425-445.
    • (1997) J Comput-Aided Mol Des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 15
    • 0028892389 scopus 로고
    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets
    • Godzik A, Kolinski A, Skolnick J. 1995. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Protein Sci 4:2107-2117.
    • (1995) Protein Sci , vol.4 , pp. 2107-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
  • 17
    • 0026655922 scopus 로고
    • Protein tertiary structure recognition using optimized Hamiltonians with local interactions
    • Goldstein RA. Luthey-Schulten ZA, Wolynes PG. 1992b. Protein tertiary structure recognition using optimized Hamiltonians with local interactions. Proc Natl Acad Sci USA 89:9029-9033.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 9029-9033
    • Goldstein, R.A.1    Luthey-Schulten, Z.A.2    Wolynes, P.G.3
  • 19
    • 0029995624 scopus 로고    scopus 로고
    • VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands
    • Head RD, Smythe ML, Oprea TI, Waller CL, Green SM, Marshall GR. 1996. VALIDATE: A new method for the receptor-based prediction of binding affinities of novel ligands. J Am Chem Soc 118:3959-3969.
    • (1996) J Am Chem Soc , vol.118 , pp. 3959-3969
    • Head, R.D.1    Smythe, M.L.2    Oprea, T.I.3    Waller, C.L.4    Green, S.M.5    Marshall, G.R.6
  • 20
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds DA, Levitt M. 1994. Exploring conformational space with a simple lattice model for protein structure. J Mol Biol 243:668-682.
    • (1994) J Mol Biol , vol.243 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 21
    • 0029942661 scopus 로고    scopus 로고
    • Structure-derived potentials for folding simulations
    • Jernigan R, Bahar I. 1996. Structure-derived potentials for folding simulations. Curr Opin Struct Biol 6:195-209.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 195-209
    • Jernigan, R.1    Bahar, I.2
  • 22
    • 0028318094 scopus 로고
    • Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches
    • Kocher JA, Rooman MJ, Wodak SJ. 1994. Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J Mol Biol 235:1598-1613.
    • (1994) J Mol Biol , vol.235 , pp. 1598-1613
    • Kocher, J.A.1    Rooman, M.J.2    Wodak, S.J.3
  • 23
    • 7044239742 scopus 로고
    • Free energy calculations - Applications to chemical and biological phenomena
    • Kollman PA. 1993. Free energy calculations - Applications to chemical and biological phenomena. Chem Rev 7:2395-2417.
    • (1993) Chem Rev , vol.7 , pp. 2395-2417
    • Kollman, P.A.1
  • 24
    • 0642301503 scopus 로고    scopus 로고
    • Challenges and prospects for computational aids to molecular diversity
    • Martin YC. 1997. Challenges and prospects for computational aids to molecular diversity. Perspect Drug Discovery Des 7/8:159-172.
    • (1997) Perspect Drug Discovery Des , vol.7-8 , pp. 159-172
    • Martin, Y.C.1
  • 26
    • 0001052814 scopus 로고    scopus 로고
    • A comparative study of existing and new design techniques for protein models
    • Micheletti C, Maritan A, Banavar JR. 1999. A comparative study of existing and new design techniques for protein models. J Chem Phys 110:9730-9738.
    • (1999) J Chem Phys , vol.110 , pp. 9730-9738
    • Micheletti, C.1    Maritan, A.2    Banavar, J.R.3
  • 27
    • 0030596063 scopus 로고    scopus 로고
    • How to derive a protein folding potential? A new approach to an old problem
    • Mirny LA, Shakhnovich EI. 1996. How to derive a protein folding potential? A new approach to an old problem. J Mol Biol 264:1164-1179.
    • (1996) J Mol Biol , vol.264 , pp. 1164-1179
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 28
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential
    • Mitchell JBO, Laskowski RA, Alex A, Thornton JM. 1999. BLEEP - Potential of mean force describing protein-ligand interactions: I. Generating potential. J Comput Chem 20:1165-1176.
    • (1999) J Comput Chem , vol.20 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Thornton, J.M.4
  • 29
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • Miyazawa S, Jernigan RL. 1985. Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18:534-552.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 30
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge I, Martin YC. 1999. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J Med Chem 42:791-804.
    • (1999) J Med Chem , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 31
    • 0026717932 scopus 로고
    • Free energy perturbation studies on inhibitor binding to HIV-I proteinase
    • Rao BG, Tilton RF, Singh UC. 1992. Free energy perturbation studies on inhibitor binding to HIV-I proteinase. J Am Chem Soc 114:4447-4452.
    • (1992) J Am Chem Soc , vol.114 , pp. 4447-4452
    • Rao, B.G.1    Tilton, R.F.2    Singh, U.C.3
  • 33
    • 0025341310 scopus 로고
    • Calculation of conformational ensemble from potential of mean force. An approach to knowledge-based prediction of local structures in globular proteins
    • Sippl MJ. 1990. Calculation of conformational ensemble from potential of mean force. An approach to knowledge-based prediction of local structures in globular proteins. J Mol Biol 213:859-883.
    • (1990) J Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 34
    • 0030342727 scopus 로고    scopus 로고
    • Helmholtz free energies of atom pair interactions in proteins
    • Sippl MJ, Ortner M, Jaritz M. Lackner P. 1996. Helmholtz free energies of atom pair interactions in proteins. Fold Des 8:289-298.
    • (1996) Fold Des , vol.8 , pp. 289-298
    • Sippl, M.J.1    Ortner, M.2    Jaritz, M.3    Lackner, P.4
  • 35
    • 0029976427 scopus 로고    scopus 로고
    • Statistical potentials extracted from protein structures: How accurate are they?
    • Thomas PD, Dill KA. 1996. Statistical potentials extracted from protein structures: How accurate are they? J Mol Biol 257:457-469.
    • (1996) J Mol Biol , vol.257 , pp. 457-469
    • Thomas, P.D.1    Dill, K.A.2
  • 36
    • 0028881193 scopus 로고
    • Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
    • Verkhivker G, Appelt K, Freer ST, Villafranca JE. 1995. Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng 8: 667-691.
    • (1995) Protein Eng , vol.8 , pp. 667-691
    • Verkhivker, G.1    Appelt, K.2    Freer, S.T.3    Villafranca, J.E.4
  • 37
    • 0029119320 scopus 로고
    • A preference-based free-energy parametrization of enzyme-inhibitor binding-application to HIV-1 protease inhibitor design
    • Wallquist A, Jernigan R, Covell D. 1995. A preference-based free-energy parametrization of enzyme-inhibitor binding-application to HIV-1 protease inhibitor design. Protein Sci 4: 1881-1903.
    • (1995) Protein Sci , vol.4 , pp. 1881-1903
    • Wallquist, A.1    Jernigan, R.2    Covell, D.3


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