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Volumn 329, Issue 1, 2003, Pages 159-174

A novel approach to decoy set generation: Designing a physical energy function having local minima with native structure characteristics

Author keywords

Ab initio; Conformation; Energy function; Local minima; Optimization

Indexed keywords

PROTEIN; SOLVENT;

EID: 0038708222     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00323-1     Document Type: Article
Times cited : (80)

References (25)
  • 1
    • 0016610491 scopus 로고
    • Computer simulation of protein folding
    • Levitt M., Warshel A. Computer simulation of protein folding. Nature. 253:1975;694-698.
    • (1975) Nature , vol.253 , pp. 694-698
    • Levitt, M.1    Warshel, A.2
  • 2
    • 0043288195 scopus 로고
    • Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence
    • Burgess A.Y., Scheraga H.A. Assessment of some problems associated with prediction of the three-dimensional structure of a protein from its amino-acid sequence. Proc. Natl Acad. Sci. USA. 72:1975;1221-1225.
    • (1975) Proc. Natl Acad. Sci. USA , vol.72 , pp. 1221-1225
    • Burgess, A.Y.1    Scheraga, H.A.2
  • 3
    • 0032620117 scopus 로고    scopus 로고
    • Improved ab initio predictions with a simplified, flexible geometry model
    • Osguthorpe D.J. Improved ab initio predictions with a simplified, flexible geometry model. Proteins: Struct. Funct. Genet. 1999;186-193.
    • (1999) Proteins: Struct. Funct. Genet. , pp. 186-193
    • Osguthorpe, D.J.1
  • 5
  • 6
    • 0031556019 scopus 로고    scopus 로고
    • Protein folding simulations with genetic algorithms and a detailed molecular description
    • Pedersen J.T., Moult J. Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269:1997;240-259.
    • (1997) J. Mol. Biol. , vol.269 , pp. 240-259
    • Pedersen, J.T.1    Moult, J.2
  • 7
    • 0000594925 scopus 로고
    • The multiple minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method
    • Piela L., Kostrowicki J., Scheraga H.A. The multiple minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method. J. Phys. Chem. 93:1989;3339-3346.
    • (1989) J. Phys. Chem. , vol.93 , pp. 3339-3346
    • Piela, L.1    Kostrowicki, J.2    Scheraga, H.A.3
  • 8
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
    • Park B., Levitt M. Energy functions that discriminate X-ray and near-native folds from well-constructed decoys. J. Mol. Biol. 258:1996;367-392.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.1    Levitt, M.2
  • 9
    • 0028149160 scopus 로고
    • Exploring conformational space with a simple lattice model for protein structure
    • Hinds D.A., Levitt M. Exploring conformational space with a simple lattice model for protein structure. J. Mol. Biol. 243:1994;668-682.
    • (1994) J. Mol. Biol. , vol.243 , pp. 668-682
    • Hinds, D.A.1    Levitt, M.2
  • 10
    • 0029063717 scopus 로고
    • The complexity and accuracy of discrete state models of protein structure
    • Park B.H., Levitt M. The complexity and accuracy of discrete state models of protein structure. J. Mol. Biol. 249:1995;493-507.
    • (1995) J. Mol. Biol. , vol.249 , pp. 493-507
    • Park, B.H.1    Levitt, M.2
  • 11
    • 0035847003 scopus 로고    scopus 로고
    • A novel method for sampling alpha-helical protein backbones
    • Fain B., Levitt M. A novel method for sampling alpha-helical protein backbones. J. Mol. Biol. 305:2001;191-201.
    • (2001) J. Mol. Biol. , vol.305 , pp. 191-201
    • Fain, B.1    Levitt, M.2
  • 12
    • 0032147142 scopus 로고    scopus 로고
    • Recognition of native structure from complete enumeration of low-resolution models with constraints
    • Ozkan B., Bahar I. Recognition of native structure from complete enumeration of low-resolution models with constraints. Proteins: Struct. Funct. Genet. 32:1998;211-222.
    • (1998) Proteins: Struct. Funct. Genet. , vol.32 , pp. 211-222
    • Ozkan, B.1    Bahar, I.2
  • 14
    • 0035830958 scopus 로고    scopus 로고
    • Prospects for ab initio protein structural genomics
    • Simons K.T., Strauss C., Baker D. Prospects for ab initio protein structural genomics. J. Mol. Biol. 306:2001;1191-1199.
    • (2001) J. Mol. Biol. , vol.306 , pp. 1191-1199
    • Simons, K.T.1    Strauss, C.2    Baker, D.3
  • 15
    • 0000467663 scopus 로고    scopus 로고
    • Finding the needle in a haystack: Educing native folds from ambiguous ab initio protein structure predictions
    • Betancourt M.R., Skolnick J. Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J. Comput. Chem. 22:2001;339-353.
    • (2001) J. Comput. Chem. , vol.22 , pp. 339-353
    • Betancourt, M.R.1    Skolnick, J.2
  • 16
    • 0031728015 scopus 로고    scopus 로고
    • Efficient dynamics in the space of contact maps
    • Vendruscolo M., Domany E. Efficient dynamics in the space of contact maps. Fold. Des. 3:1998;329-336.
    • (1998) Fold. Des. , vol.3 , pp. 329-336
    • Vendruscolo, M.1    Domany, E.2
  • 17
    • 0014825610 scopus 로고
    • New approach to variable metric algorithms
    • Fletcher R. New approach to variable metric algorithms. Comput. J. 13:1970;317-322.
    • (1970) Comput. J. , vol.13 , pp. 317-322
    • Fletcher, R.1
  • 18
    • 0021095856 scopus 로고
    • Protein folding by restrained energy minimization and molecular dynamics
    • Levitt M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170:1983;723-764.
    • (1983) J. Mol. Biol. , vol.170 , pp. 723-764
    • Levitt, M.1
  • 19
    • 0000171351 scopus 로고    scopus 로고
    • Pairwise contact potentials are unsuitable for protein folding1
    • Vendruscolo M., Domany E. Pairwise contact potentials are unsuitable for protein folding1. J. Chem. Phys. 109:1998;11101-11108.
    • (1998) J. Chem. Phys. , vol.109 , pp. 11101-11108
    • Vendruscolo, M.1    Domany, E.2
  • 20
    • 0031757623 scopus 로고    scopus 로고
    • Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations
    • Keasar C., Rosenfeld R. Empirical modifications to the Amber/OPLS potential for predicting the solution conformations of cyclic peptides by vacuum calculations. Fold. Des. 3:1998;379-388.
    • (1998) Fold. Des. , vol.3 , pp. 379-388
    • Keasar, C.1    Rosenfeld, R.2
  • 21
    • 0034733381 scopus 로고    scopus 로고
    • Ab initio construction of protein tertiary structures using a hierarchical approach
    • Xia Y., Huang E.S., Levitt M., Samudrala R. Ab initio construction of protein tertiary structures using a hierarchical approach. J. Mol. Biol. 300:2000;171-185.
    • (2000) J. Mol. Biol. , vol.300 , pp. 171-185
    • Xia, Y.1    Huang, E.S.2    Levitt, M.3    Samudrala, R.4
  • 23
    • 0035314042 scopus 로고    scopus 로고
    • Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation
    • Bonneau R., Strauss C.E.M., Baker D. Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins: Struct. Funct. Genet. 43:2001;1-11.
    • (2001) Proteins: Struct. Funct. Genet. , vol.43 , pp. 1-11
    • Bonneau, R.1    Strauss, C.E.M.2    Baker, D.3
  • 24
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R., Molt J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275:1998;895-916.
    • (1998) J. Mol. Biol. , vol.275 , pp. 895-916
    • Samudrala, R.1    Molt, J.2
  • 25
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18:1997;2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.