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Volumn 82, Issue SUPPL.2, 2014, Pages 188-195

Protein structure modeling for CASP10 by multiple layers of global optimization

Author keywords

CASP; Energy function; Global optimization; High accuracy modeling; Homology modeling; Side chain modeling; Structure prediction; Template based modeling

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; HUMAN; HYDROGEN BOND; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; QUALITY CONTROL; RANDOM FOREST;

EID: 84893009061     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24397     Document Type: Article
Times cited : (39)

References (19)
  • 1
    • 36749030503 scopus 로고    scopus 로고
    • High accuracy template based modeling by global optimization
    • Joo K, Lee J, Lee S, Seo, J-H, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins 2007;69 (Suppl 8):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
    • 69849109596 scopus 로고    scopus 로고
    • All-atom chain-building by optimizing MODELLER energy function using conformational space annealing
    • Joo K, Lee J, Seo J-H, Lee K, Kim B-G, Lee J. All-atom chain-building by optimizing MODELLER energy function using conformational space annealing. Proteins 2009;75:1010-1023.
    • (2009) Proteins , vol.75 , pp. 1010-1023
    • Joo, K.1    Lee, J.2    Seo, J.-H.3    Lee, K.4    Kim, B.-G.5    Lee, J.6
  • 3
    • 58149279530 scopus 로고    scopus 로고
    • Multiple sequence alignment by conformational space annealing
    • Joo K, Lee J, Kim I, Lee SJ, Lee J. Multiple sequence alignment by conformational space annealing. Biophys J 2008;95:4813-4819.
    • (2008) Biophys J , vol.95 , pp. 4813-4819
    • Joo, K.1    Lee, J.2    Kim, I.3    Lee, S.J.4    Lee, J.5
  • 4
    • 79960101915 scopus 로고    scopus 로고
    • De novo protein structure prediction by dynamic fragment assembly and conformational space annealing
    • Lee J, Lee J, Sasaki TN, Sasai M, Seok C, Lee J. De novo protein structure prediction by dynamic fragment assembly and conformational space annealing. Proteins 2011;79:2403-2417.
    • (2011) Proteins , vol.79 , pp. 2403-2417
    • Lee, J.1    Lee, J.2    Sasaki, T.N.3    Sasai, M.4    Seok, C.5    Lee, J.6
  • 5
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 6
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
    • (2003) J Mol Biol , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 7
    • 80054694711 scopus 로고    scopus 로고
    • GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction
    • Zhou H, Skolnick J. GOAP: a generalized orientation-dependent, all-atom statistical potential for protein structure prediction. Biophys J 2011;101:2043-2052.
    • (2011) Biophys J , vol.101 , pp. 2043-2052
    • Zhou, H.1    Skolnick, J.2
  • 8
    • 0001176785 scopus 로고    scopus 로고
    • New optimization method for conformational energy calculations on polypeptides: conformational space annealing
    • Lee J, Scheraga HA, Rackovsky S. New optimization method for conformational energy calculations on polypeptides: conformational space annealing. J Comput Chem 1997;18:1222-1232.
    • (1997) J Comput Chem , vol.18 , pp. 1222-1232
    • Lee, J.1    Scheraga, H.A.2    Rackovsky, S.3
  • 9
    • 84892954114 scopus 로고    scopus 로고
    • Orry AJW, Abagyan R, editors. Humana Press, New York
    • Orry AJW, Abagyan R, editors. Homology modeling: methods and protocols. Humana Press, New York, 2012.
    • (2012) Homology modeling: methods and protocols
  • 10
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
    • (1993) J Mol Biol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 11
    • 84861945707 scopus 로고    scopus 로고
    • Modularity optimization by conformational space annealing
    • Lee J, Gross SP, Lee J. Modularity optimization by conformational space annealing. Phys Rev E 2012;85:056702.
    • (2012) Phys Rev E , vol.85 , pp. 056702
    • Lee, J.1    Gross, S.P.2    Lee, J.3
  • 12
    • 0031829993 scopus 로고    scopus 로고
    • Coffee: an objective function for multiple sequence alignments
    • Notredame C, Holm L, Higgins DG. Coffee: an objective function for multiple sequence alignments. Bioinformatics 1998;14:407-422.
    • (1998) Bioinformatics , vol.14 , pp. 407-422
    • Notredame, C.1    Holm, L.2    Higgins, D.G.3
  • 13
    • 17644392830 scopus 로고    scopus 로고
    • Tm-align: a protein structure alignment algorithm based on the TM-score
    • Zhang Y, Skolnick J. Tm-align: a protein structure alignment algorithm based on the TM-score. Nucl Acids Res 2005;33:2302-2309.
    • (2005) Nucl Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 14
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman L. Random forests. Mach Learn 2001;45:5-32.
    • (2001) Mach Learn , vol.45 , pp. 5-32
    • Breiman, L.1
  • 15
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 16
    • 84862184719 scopus 로고    scopus 로고
    • SANN: solvent accessibility prediction of proteins by nearest neighbor method
    • Joo K, Lee SJ, Lee J. SANN: solvent accessibility prediction of proteins by nearest neighbor method. Proteins 2012;80:1791-1797.
    • (2012) Proteins , vol.80 , pp. 1791-1797
    • Joo, K.1    Lee, S.J.2    Lee, J.3
  • 17
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 18
    • 0043180474 scopus 로고    scopus 로고
    • PISCES: a protein sequence culling server
    • Wang G, Dunbrack RL, Jr. PISCES: a protein sequence culling server. Bioinformatics 2003;19:1589-1591.
    • (2003) Bioinformatics , vol.19 , pp. 1589-1591
    • Wang, G.1    Dunbrack Jr., R.L.2
  • 19
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • Canutescu AA, Shelenkov AA, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003;12:2001-2014.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.