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Volumn 41, Issue 4, 2000, Pages 518-534

Discrimination of near-native protein structures from misfolded models by empirical free energy functions

Author keywords

Free energy function; Implicit solvation; Molecular mechanics; Protein structure determination; Structure based potential

Indexed keywords

ARTICLE; ENERGY; ENTROPY; MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SOLVATION;

EID: 0034560338     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20001201)41:4<518::AID-PROT90>3.0.CO;2-6     Document Type: Article
Times cited : (68)

References (66)
  • 11
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazava, S.1    Jernigan, R.2
  • 18
    • 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
  • 19
    • 0000188290 scopus 로고    scopus 로고
    • Evaluation of atomic level mean force potentials via inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
    • (1996) Prot Eng , vol.8 , pp. 175-186
    • DeBolt, E.E.1    Skolnick, J.2
  • 23
    • 0029132872 scopus 로고
    • A genetic algorithm that seeks native states of peptides and proteins
    • (1995) Biophys J , vol.69 , pp. 340-355
    • Sun, S.1
  • 24
    • 0032461411 scopus 로고    scopus 로고
    • Selecting near-native conformations in homology modeling: The role of molecular mechanics and solvation terms
    • (1997) Prot Sci , vol.7 , pp. 1772-1780
    • Janardhan, A.1    Vajda, S.2
  • 26
    • 0028804966 scopus 로고
    • Simulating the folding of small proteins by use of the local minimum energy and the free solvation energy yields native-like structures
    • (1995) J Mol Graphics , vol.13 , pp. 312-322
    • Brasseur, R.1
  • 28
    • 0023779259 scopus 로고
    • Calculation 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
  • 33
    • 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
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 34
    • 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
  • 36
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
    • (1997) Prot Sci , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 40
    • 0029414725 scopus 로고
    • Extracting hydrophobicity parameters from solute partition and protein mutation/unfolding experiments
    • (1995) Prot Eng , vol.8 , pp. 1081-1092
    • Vajda, S.1    Weng, Z.2    DeLisi, C.3
  • 43
    • 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
  • 53
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • (1994) J Mol Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 58
    • 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
  • 62
    • 0022788691 scopus 로고
    • An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
    • (1986) Proteins , vol.1 , pp. 146-163
    • Moult, J.1    James, M.N.G.2
  • 66


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.