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Volumn 8, Issue 7, 2013, Pages

i3Drefine Software for Protein 3D Structure Refinement and Its Assessment in CASP10

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOMETRY; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; CRITICAL ASSESSMENT OF PROTEIN STRUCTURE PREDICTION; HYDROGEN BOND; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PROTEIN STRUCTURE; THREE DIMENSIONAL IMAGING;

EID: 84880487307     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0069648     Document Type: Article
Times cited : (50)

References (31)
  • 11
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL, (2007) Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins: Structure, Function, and Bioinformatics 67: 922-930.
    • (2007) Proteins: Structure, Function, and Bioinformatics , vol.67 , pp. 922-930
    • Chen, J.1    Brooks, C.L.2
  • 12
    • 0347994106 scopus 로고    scopus 로고
    • Refinement of homology-based protein structures by molecular dynamics simulation techniques
    • Fan H, Mark AE, (2009) Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Science 13: 211-220.
    • (2009) Protein Science , vol.13 , pp. 211-220
    • Fan, H.1    Mark, A.E.2
  • 13
    • 45849124627 scopus 로고    scopus 로고
    • Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations
    • Ishitani R, Terada T, Shimizu K, (2008) Refinement of comparative models of protein structure by using multicanonical molecular dynamics simulations. Molecular Simulation 34: 327-336.
    • (2008) Molecular Simulation , vol.34 , pp. 327-336
    • Ishitani, R.1    Terada, T.2    Shimizu, K.3
  • 15
    • 14644438345 scopus 로고    scopus 로고
    • Progress and challenges in high-resolution refinement of protein structure models
    • Misura K, Baker D, (2005) Progress and challenges in high-resolution refinement of protein structure models. Proteins: Structure, Function, and Bioinformatics 59: 15-29.
    • (2005) Proteins: Structure, Function, and Bioinformatics , vol.59 , pp. 15-29
    • Misura, K.1    Baker, D.2
  • 19
    • 43149099005 scopus 로고    scopus 로고
    • Development of a physics-based force field for the scoring and refinement of protein models
    • Wroblewska L, Jagielska A, Skolnick J, (2008) Development of a physics-based force field for the scoring and refinement of protein models. Biophysical journal 94: 3227-3240.
    • (2008) Biophysical Journal , vol.94 , pp. 3227-3240
    • Wroblewska, L.1    Jagielska, A.2    Skolnick, J.3
  • 22
    • 33646887390 scopus 로고
    • On the limited memory BFGS method for large scale optimization
    • Liu DC, Nocedal J, (1989) On the limited memory BFGS method for large scale optimization. Mathematical programming 45: 503-528.
    • (1989) Mathematical Programming , vol.45 , pp. 503-528
    • Liu, D.C.1    Nocedal, J.2
  • 23
    • 0029633167 scopus 로고
    • Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution
    • Levitt M, Hirshberg M, Sharon R, Daggett V, (1995) Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution. Computer Physics Communications 91: 215-231.
    • (1995) Computer Physics Communications , vol.91 , pp. 215-231
    • Levitt, M.1    Hirshberg, M.2    Sharon, R.3    Daggett, V.4
  • 24
  • 25
    • 82955239912 scopus 로고    scopus 로고
    • Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling
    • Zhang J, Liang Y, Zhang Y, (2011) Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling. Structure 19: 1784-1795.
    • (2011) Structure , vol.19 , pp. 1784-1795
    • Zhang, J.1    Liang, Y.2    Zhang, Y.3
  • 26
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 27
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • Zemla A, (2003) LGA: a method for finding 3D similarities in protein structures. Nucleic acids research 31: 3370-3374.
    • (2003) Nucleic Acids Research , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 31
    • 0031560777 scopus 로고    scopus 로고
    • Contact area difference (CAD): a robust measure to evaluate accuracy of protein models
    • Abagyan RA, Totrov MM, (1997) Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. Journal of molecular biology 268: 678-685.
    • (1997) Journal of Molecular Biology , vol.268 , pp. 678-685
    • Abagyan, R.A.1    Totrov, M.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.