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Volumn 48, Issue 2, 2002, Pages 404-422

Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model

Author keywords

Fold recognition; Protein decoys; Protein solvation

Indexed keywords

ARTICLE; ELECTRICITY; ENERGY; MATHEMATICAL MODEL; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; SEQUENCE HOMOLOGY; SOLVATION;

EID: 0036681394     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10171     Document Type: Article
Times cited : (110)

References (103)
  • 2
    • 0025341310 scopus 로고
    • Calculation of conformational ensembles from potentials of mean force: An approach to the knowledge-based prediction of local structures in globular proteins
    • (1990) Mol Biol , vol.213 , pp. 859-883
    • Sippl, M.J.J.1
  • 3
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential. Hydrophobic potential derived from x-ray structure of globular proteins is able to identify native folds
    • (1992) Mol Biol , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.J.J.2
  • 9
    • 0034308163 scopus 로고    scopus 로고
    • Distance-dependent, pair potential for protein folding: Results from linear optimization
    • (2000) Proteins , vol.41 , pp. 40-46
    • Tobi, D.1    Elber, R.2
  • 11
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • (1999) J Mol Biol , vol.288 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 12
    • 0034486196 scopus 로고    scopus 로고
    • Free energy determinants of tertiary structure and the evaluation of protein models
    • (2000) Protein Sci , vol.9 , pp. 2181-2191
    • Petrey, D.1    Honig, B.2
  • 16
    • 0032233055 scopus 로고    scopus 로고
    • Computer simulation with explicit solvent: Recent progress in the thermodynamic decomposition of free energies and in modeling electrostatic effects
    • (1998) Annu Rev Phys Chem , vol.49 , pp. 531-567
    • Levy, R.M.1    Gallicchio, E.2
  • 21
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvation based on pairwise descreening of solute atomic charges from a dielectric medium
    • (1996) J Phys Chem , vol.100 , pp. 19824-19839
    • Hawkins, G.1    Cramer, C.2    Truhlar, D.3
  • 32
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • (1999) J Biophys Chem , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 33
    • 0023779259 scopus 로고
    • Calculations of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
    • (1988) Proteins , vol.4 , pp. 7-18
    • Gilson, M.K.1    Honig, B.2
  • 35
    • 26844574873 scopus 로고
    • Hydration phenomena, classical electrostatics, and the boundary element method
    • (1990) J Phys Chem , vol.94 , pp. 1725-1733
    • Rashin, A.A.1
  • 44
    • 34250928962 scopus 로고
    • Volumes and heats of hydration of ions
    • (1920) Physik , vol.1 , pp. 45-48
    • Born, M.Z.1
  • 52
    • 0009741406 scopus 로고    scopus 로고
    • Exploratory studies of ab initio protein structure prediction: Multiple copy simulated annealing, AMBER energy functions, and a generalized Born/solvent accessibility solvation model
    • In press
    • (2001) Proteins
    • Liu, Y.1    Beveridge, D.L.2
  • 56
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and and an unfavorable high packing density term, for simulation and threading
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.J.2
  • 58
    • 0033566614 scopus 로고    scopus 로고
    • An empirical energy potential with a reference state for protein fold and sequence recognition
    • (1999) Protein , vol.36 , pp. 357-369
    • Miyazawa, S.1    Jernigan, R.L.2
  • 60
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate x-ray and near-native folds from well-constructed decoys
    • (1996) J Mol Biol , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 61
    • 0032147142 scopus 로고    scopus 로고
    • Recognition of native structures from complete enumeration of low-resolution models with constraints
    • (1998) Proteins , vol.32 , pp. 211-222
    • Ozkan, B.1    Bahar, I.2
  • 62
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • (1998) J Mol Biol , vol.275 , pp. 895-916
    • Samudrala, R.1    Moult, J.2
  • 73
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit continuum solvent
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 77
  • 81
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • (2000) Proteins , vol.39 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 85
    • 0026754015 scopus 로고
    • Accurate modeling of protein conformation by automatic segment matching
    • (1992) J Mol Biol , vol.226 , pp. 507-533
    • Levitt, M.1
  • 87
  • 91
    • 0019522383 scopus 로고
    • Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-Å resolution
    • (1981) Biochemistry , vol.20 , pp. 2361-2370
    • Deisenhofer, J.1
  • 101


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