메뉴 건너뛰기




Volumn 11, Issue 2, 2002, Pages 430-448

Statistical potentials for fold assessment

Author keywords

Comparative modeling; Fold assessment; Fold assignment; Large scale protein structure modeling; Model evaluation; Statistical potentials

Indexed keywords

PROTEIN;

EID: 0036145846     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.25502     Document Type: Article
Times cited : (313)

References (111)
  • 2
    • 0032126517 scopus 로고    scopus 로고
    • Generalized affine gap costs for protein sequence alignment
    • (1998) Proteins , vol.32 , pp. 88-96
    • Altschul, S.1
  • 3
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • (1997) J. Mol. Biol. , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.2
  • 8
    • 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
    • (1999) Protein Sci. , vol.8 , pp. 361-369
    • Betancourt, M.1    Thirumalai, D.2
  • 15
    • 0026016378 scopus 로고
    • The frequency of ion-pair substructures in proteins is quantitatively related to electrostatic potential: A statistical model for nonbonded interactions
    • (1991) Proteins , vol.9 , pp. 108-119
    • Bryant, S.H.1    Lawrence, C.E.2
  • 16
    • 0027318317 scopus 로고
    • An empirical energy function for threading protein sequence through the folding motif
    • (1993) Proteins , vol.16 , pp. 92-112
  • 17
    • 0026539511 scopus 로고
    • Structure-derived hydrophobic potential. Hydrophobic potential derived from x-ray structures of globular proteins is able to identify native folds
    • (1992) J. Mol. Biol. , vol.224 , pp. 725-732
    • Casari, G.1    Sippl, M.2
  • 19
    • 0034333083 scopus 로고    scopus 로고
    • How to generate improved potentials for protein tertiary structure prediction: A lattice model study
    • (2000) Proteins , vol.41 , pp. 157-163
    • Chiu, T.1    Goldstein, R.2
  • 22
    • 0029844461 scopus 로고    scopus 로고
    • Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: Atomic burial position and pairwise non-bonded interactions
    • (1996) Protein Eng. , vol.9 , pp. 937-955
    • DeBolt, S.E.1    Skolnick, J.2
  • 27
    • 0032080720 scopus 로고    scopus 로고
    • Influence of protein structure databases on the predictive power of statistical pair potentials
    • (1998) Proteins , vol.31 , pp. 139-149
    • Furuichi, E.1    Koehl, P.2
  • 29
    • 0029873155 scopus 로고    scopus 로고
    • Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials
    • (1996) J. Mol. Biol. , vol.257 , pp. 1112-1126
    • Gilis, D.1    Rooman, M.2
  • 30
    • 0030777760 scopus 로고    scopus 로고
    • Predicting protein stability changes upon mutation using data-base-derived potentials: Solvent accessibility determines the importance of local versus non-local interactions along the sequence
    • (1997) J. Mol. Biol. , vol.272 , pp. 276-290
  • 31
    • 0035255016 scopus 로고    scopus 로고
    • Identification and ab initio simulations of early folding units in proteins
    • (2001) Proteins , vol.42 , pp. 164-176
  • 38
    • 0031298075 scopus 로고    scopus 로고
    • Successful ab initio prediction of the tertiary structure of nk-lysin using multiple sequences and recognized supersecondary structural motifs
    • (1997) Proteins , vol.1 , Issue.SUPPL. , pp. 185-191
    • Jones, D.1
  • 39
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
  • 40
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
  • 44
    • 0028063257 scopus 로고
    • Polar and nonpolar atomic environments in the protein core: Implication for folding and binding
    • (1994) Proteins , vol.20 , pp. 264-278
    • Koehl, P.1    Delarue, M.2
  • 49
    • 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
  • 50
  • 51
    • 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.1    Duan, Y.2    Kollman, P.3
  • 57
    • 0032540222 scopus 로고    scopus 로고
    • Assessing protein structures with a non-local atomic interaction energy
    • (1998) J. Mol. Biol. , vol.277 , pp. 1141-1152
  • 58
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term 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.2
  • 59
    • 0033867374 scopus 로고    scopus 로고
    • Identifying sequence-structure pairs undetected by sequence alignments
    • (2000) Protein Eng. , vol.13 , pp. 459-475
  • 65
    • 0030634582 scopus 로고    scopus 로고
    • Tertiary structure prediction using meanforce potentials and internal energy functions: Successful prediction for coiled-coil geometries
    • (1997) Fold Des. , vol.2
    • O'Donoghue, S.1    Nilges, M.2
  • 70
    • 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
  • 73
    • 0034486196 scopus 로고    scopus 로고
    • Free energy determinants of tertiary structure and the evaluation of protein models
    • (2000) Prot. Sci. , vol.9 , pp. 2181-2191
    • Petrey, D.1    Honig, B.2
  • 78
    • 0033135619 scopus 로고    scopus 로고
    • Prediction of loop geometries using a generalized Born model of solvation effects
    • (1999) Proteins , vol.35 , pp. 173-183
    • Rapp, C.1    Friesner, R.2
  • 81
    • 0029563695 scopus 로고
    • Are database-derived potentials valid for scoring both forward and inverted protein folding?
    • (1995) Protein Eng. , vol.8 , pp. 849-858
    • Rooman, M.1    Wodak, S.2
  • 82
    • 0032523791 scopus 로고    scopus 로고
    • Different derivations of knowledge-based potentials and analysis of their robustness and context-dependent predictive power
    • (1998) Eur. J. Biochem. , vol.254 , pp. 135-143
    • Rooman, M.1    Gilis, D.2
  • 83
    • 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
  • 85
    • 0042624145 scopus 로고    scopus 로고
    • Comparative protein structure modeling in genomics
    • (1999) J. Comp. Phys. , vol.151 , pp. 388-401
  • 90
    • 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) J. Mol. Biol. , vol.213 , pp. 859-883
    • Sippl, M.J.1
  • 91
    • 0027650879 scopus 로고
    • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures
    • (1993) J. Comp. Aid. Molec. Design , vol.7 , pp. 473-501
  • 92
    • 0026704815 scopus 로고
    • Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations
    • (1992) Proteins , vol.13 , pp. 258-271
    • Sippl, M.J.1    Weitckus, S.2
  • 95
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
    • (1993) Protein Sci. , vol.2 , pp. 762-785
    • Sun, S.1
  • 98
    • 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
  • 106
    • 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 solvent continuum model
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 109
    • 0034602373 scopus 로고    scopus 로고
    • Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
    • (2000) J. Mol. Biol. , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.