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Volumn 369, Issue 2, 2008, Pages 500-506

A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction

Author keywords

Fragment assembly; Langevin dynamics; Protein structure prediction

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE;

EID: 40849086146     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.02.048     Document Type: Article
Times cited : (8)

References (30)
  • 1
    • 36749030503 scopus 로고    scopus 로고
    • High accuracy template based modeling by global optimization
    • Joo K., Lee J., Lee S., Seo J.-H., Lee S.J., and Lee J. High accuracy template based modeling by global optimization. Proteins 69 Suppl. 8 (2007) 83-89
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 83-89
    • Joo, K.1    Lee, J.2    Lee, S.3    Seo, J.-H.4    Lee, S.J.5    Lee, J.6
  • 2
    • 36749086922 scopus 로고    scopus 로고
    • Assessment of CASP7 structure predictions for template free targets
    • Jauch R., Yeo H.C., Kolatkar P.R., and Clarke N.D. Assessment of CASP7 structure predictions for template free targets. Proteins 69 Suppl. 8 (2007) 57-67
    • (2007) Proteins , vol.69 , Issue.SUPPL. 8 , pp. 57-67
    • Jauch, R.1    Yeo, H.C.2    Kolatkar, P.R.3    Clarke, N.D.4
  • 3
    • 33947219832 scopus 로고    scopus 로고
    • Worth the effort: an account of the seventh meeting of the worldwide critical assessment of techniques for protein structure prediction
    • Tramontano A. Worth the effort: an account of the seventh meeting of the worldwide critical assessment of techniques for protein structure prediction. FEBS J. 274 (2007) 1651-1654
    • (2007) FEBS J. , vol.274 , pp. 1651-1654
    • Tramontano, A.1
  • 5
    • 24944493938 scopus 로고    scopus 로고
    • Toward high-resolution de novo structure prediction for small proteins
    • Bradley P., Misura K.M.S., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
    • (2005) Science , vol.309 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 6
    • 14744276882 scopus 로고    scopus 로고
    • Protein structure prediction based on fragment assembly and parameter optimization
    • Lee J., Kim S.-Y., and Lee J. Protein structure prediction based on fragment assembly and parameter optimization. Biophys. Chem. 115 (2005) 209-214
    • (2005) Biophys. Chem. , vol.115 , pp. 209-214
    • Lee, J.1    Kim, S.-Y.2    Lee, J.3
  • 7
    • 30144441768 scopus 로고    scopus 로고
    • SimFold energy function for de novo protein structure prediction: consensus with Rosetta
    • Fujitsuka Y., Chikenji G., and Takada S. SimFold energy function for de novo protein structure prediction: consensus with Rosetta. Proteins 62 (2006) 381-398
    • (2006) Proteins , vol.62 , pp. 381-398
    • Fujitsuka, Y.1    Chikenji, G.2    Takada, S.3
  • 9
    • 30344488120 scopus 로고    scopus 로고
    • TASSER: an automated method for the prediction of protein tertiary structures in CASP6
    • Zhang Y., Arakaki A.K., and Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61 Suppl. 7 (2005) 91-98
    • (2005) Proteins , vol.61 , Issue.SUPPL. 7 , pp. 91-98
    • Zhang, Y.1    Arakaki, A.K.2    Skolnick, J.3
  • 10
    • 34548608483 scopus 로고    scopus 로고
    • Ab initio protein structure prediction using Chunk-TASSER
    • Zhou H., and Skolnick J. Ab initio protein structure prediction using Chunk-TASSER. Biophys. J. 93 (2007) 1510-1518
    • (2007) Biophys. J. , vol.93 , pp. 1510-1518
    • Zhou, H.1    Skolnick, J.2
  • 11
    • 34249869832 scopus 로고    scopus 로고
    • Ab initio modeling of small proteins by iterative TASSER simulations
    • Wu S., Skolnick J., and Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 5 17 (2007)
    • (2007) BMC Biol. , vol.5 , Issue.17
    • Wu, S.1    Skolnick, J.2    Zhang, Y.3
  • 13
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
    • (1973) Science , vol.181 , pp. 223-230
    • Anfinsen, C.B.1
  • 14
    • 0020972782 scopus 로고
    • Theoretical studies of protein folding
    • Go N. Theoretical studies of protein folding. Ann. Rev. Biophys. Bioeng. 12 (1983) 183-210
    • (1983) Ann. Rev. Biophys. Bioeng. , vol.12 , pp. 183-210
    • Go, N.1
  • 16
    • 33644760365 scopus 로고    scopus 로고
    • Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study
    • Chikenji G., Fujitsuka Y., and Takada S. Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study. Proc. Natl. Acad. Sci. USA 103 (2006) 3141-3146
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 3141-3146
    • Chikenji, G.1    Fujitsuka, Y.2    Takada, S.3
  • 17
    • 0036558224 scopus 로고    scopus 로고
    • Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method
    • Kazmierkiewicz R., Liwo A., and Scheraga H.A. Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J. Comput. Chem. 23 (2002) 715-723
    • (2002) J. Comput. Chem. , vol.23 , pp. 715-723
    • Kazmierkiewicz, R.1    Liwo, A.2    Scheraga, H.A.3
  • 18
    • 25644455245 scopus 로고    scopus 로고
    • Protein structure prediction with the UNRES force-field using replica-exchange Monte Carlo-with-minimization; comparison with MCM, CSA and CFMC
    • Nanias M., Chinchio M., Oldziej S., Czaplewski C., and Scheraga H.A. Protein structure prediction with the UNRES force-field using replica-exchange Monte Carlo-with-minimization; comparison with MCM, CSA and CFMC. J. Comput. Chem. 26 (2005) 1472-1486
    • (2005) J. Comput. Chem. , vol.26 , pp. 1472-1486
    • Nanias, M.1    Chinchio, M.2    Oldziej, S.3    Czaplewski, C.4    Scheraga, H.A.5
  • 19
    • 14044266389 scopus 로고    scopus 로고
    • Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains
    • Liwo A., Khalili M., and Scheraga H.A. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. USA 102 (2005) 2362-2367
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 2362-2367
    • Liwo, A.1    Khalili, M.2    Scheraga, H.A.3
  • 21
    • 0034687712 scopus 로고    scopus 로고
    • Associative memory hamiltonians for structure prediction without homology: alpha-helical proteins
    • Hardin C., Eastwood M.P., Luthey-Schulten Z., and Wolynes P.G. Associative memory hamiltonians for structure prediction without homology: alpha-helical proteins. Proc. Natl. Acad. Sci. USA 97 (2000) 14235-14240
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 14235-14240
    • Hardin, C.1    Eastwood, M.P.2    Luthey-Schulten, Z.3    Wolynes, P.G.4
  • 22
    • 11444256916 scopus 로고    scopus 로고
    • A coarse-grained Langevin molecular dynamics approach to protein structure reproduction
    • Sasaki T.N., and Sasai M. A coarse-grained Langevin molecular dynamics approach to protein structure reproduction. Chem. Phys. Lett. 402 (2005) 102-106
    • (2005) Chem. Phys. Lett. , vol.402 , pp. 102-106
    • Sasaki, T.N.1    Sasai, M.2
  • 23
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 24
    • 40849103158 scopus 로고    scopus 로고
    • Available from: .
    • Available from: .
  • 25
    • 40849127317 scopus 로고    scopus 로고
    • Available from: .
    • Available from: .
  • 27
    • 84860507958 scopus 로고    scopus 로고
    • Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms
    • Cheng J., and Baldi P. Three-stage prediction of protein beta-sheets by neural networks, alignments and graph algorithms. Bioinformatics 21 Suppl. 1 (2005) i75-i84
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Cheng, J.1    Baldi, P.2
  • 28
    • 0025950944 scopus 로고
    • Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
    • Pearson W.R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11 (1991) 635-650
    • (1991) Genomics , vol.11 , pp. 635-650
    • Pearson, W.R.1
  • 29
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 31 (2003) 3370-3374
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 30
    • 40849094968 scopus 로고    scopus 로고
    • Available from: .
    • Available from: .


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