메뉴 건너뛰기




Volumn , Issue , 2010, Pages 62-70

Protein structure alignment using elastic shape analysis

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; AUTOMATIC CLUSTERING; BACKBONE GEOMETRY; BACKBONE STRUCTURES; BONE GEOMETRY; ELASTIC SHAPES; GEODESIC PATHS; MATCHING PROCESS; OPTIMAL DEFORMATION; PRIMARY SEQUENCES; PROTEIN STRUCTURE ALIGNMENT; SECONDARY STRUCTURES;

EID: 77958059975     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1854776.1854790     Document Type: Conference Paper
Times cited : (20)

References (34)
  • 1
    • 33846074754 scopus 로고    scopus 로고
    • Sisyphus - Structural alignments for proteins with non-trivial relationships
    • A. Andreeva, A. Prlic, T. J. Hubbard, and A. G. Murzin. Sisyphus - structural alignments for proteins with non-trivial relationships. Nucleic Acids Res., 35:D253-9, 2007.
    • (2007) Nucleic Acids Res. , vol.35
    • Andreeva, A.1    Prlic, A.2    Hubbard, T.J.3    Murzin, A.G.4
  • 2
    • 77958024438 scopus 로고    scopus 로고
    • Accuracy assessment of multiple structure alignments
    • Accepted
    • C. Berbalk, C. S. Schwaiger, and P. Lackner. Accuracy assessment of multiple structure alignments. Protein Sci., Accepted.
    • Protein Sci.
    • Berbalk, C.1    Schwaiger, C.S.2    Lackner, P.3
  • 4
    • 0142143332 scopus 로고    scopus 로고
    • Mass: Multiple structural alignment by secondary structures
    • O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson. Mass: multiple structural alignment by secondary structures. Bioinformatics, 19:i95-104, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 95-104
    • Dror, O.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.4
  • 5
    • 33646138726 scopus 로고    scopus 로고
    • Development and validation of a consistency based multiple structure alignment algorithm
    • J. Ebert and D. Brutlag. Development and validation of a consistency based multiple structure alignment algorithm. Bioinformatics, 22:1080-7, 2006.
    • (2006) Bioinformatics , vol.22 , pp. 1080-1087
    • Ebert, J.1    Brutlag, D.2
  • 6
    • 0032530836 scopus 로고    scopus 로고
    • A database of macromolecular motions
    • M. Gerstein and W. Krebs. A database of macromolecular motions. Nucleic Acids Res, 26:4280-90, 1998.
    • (1998) Nucleic Acids Res , vol.26 , pp. 4280-4290
    • Gerstein, M.1    Krebs, W.2
  • 7
    • 0029936121 scopus 로고    scopus 로고
    • Surprising similarities in structure comparison
    • J. F. Gibrat, T. Madej, and S. H. Bryant. Surprising similarities in structure comparison. Curr Opin Struct Biol, 6:377-85, 1996.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 377-385
    • Gibrat, J.F.1    Madej, T.2    Bryant, S.H.3
  • 8
    • 0033824470 scopus 로고    scopus 로고
    • Dalilite workbench for protein structure comparison
    • L. Holm and J. Park. Dalilite workbench for protein structure comparison. Bionformatics, 16:566-567, 2000.
    • (2000) Bionformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 9
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • L. Holm and C. Sander. Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233:123-138, 1993.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 11
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • W. Kabsch and C. Sander. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22(12):2577ÍC637, 1983.
    • (1983) Biopolymers , vol.22 , Issue.12
    • Kabsch, W.1    Sander, C.2
  • 14
    • 13444279981 scopus 로고    scopus 로고
    • Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures
    • R. Kolodny, P. Koehl, and M. Levitt. Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. J. Mol. Biol., 346:1173-88, 2005.
    • (2005) J. Mol. Biol. , vol.346 , pp. 1173-88
    • Kolodny, R.1    Koehl, P.2    Levitt, M.3
  • 16
    • 1842781469 scopus 로고    scopus 로고
    • Protein structure comparison in 3d based on secondary structure matching (ssm) followed by c-alpha alignment, scored by a new structural similarity function
    • E. Krissinel and K. Henrick. Protein structure comparison in 3d based on secondary structure matching (ssm) followed by c-alpha alignment, scored by a new structural similarity function. In In Proceedings of the Fifth international Conference on Molecular Structural Biology, 2003.
    • (2003) Proceedings of the Fifth International Conference on Molecular Structural Biology
    • Krissinel, E.1    Henrick, K.2
  • 18
    • 34548304928 scopus 로고    scopus 로고
    • Comparative analysis of protein structure alignments
    • G. Mayr, F. S. Domingues, and P. Lackner. Comparative analysis of protein structure alignments. BMC Struct Biol., 26:7:50, 2007.
    • (2007) BMC Struct Biol. , vol.26 , Issue.7 , pp. 50
    • Mayr, G.1    Domingues, F.S.2    Lackner, P.3
  • 19
    • 51849139041 scopus 로고    scopus 로고
    • Alignment of protein structures in the presence of domain motions
    • R. Mosca, B. Brannetti, and T. R. Schneider. Alignment of protein structures in the presence of domain motions. BMC Bioinformatics, 9:352, 2008.
    • (2008) BMC Bioinformatics , vol.9 , pp. 352
    • Mosca, R.1    Brannetti, B.2    Schneider, T.R.3
  • 20
    • 48449084095 scopus 로고    scopus 로고
    • Rapido: A web server for the alignment of protein structures in the presence of conformational changes
    • R. Mosca and T. R. Schneider. Rapido: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Res, 36:W42-6, 2008.
    • (2008) Nucleic Acids Res , vol.36
    • Mosca, R.1    Schneider, T.R.2
  • 21
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia. Scop: a structural classification of proteins database for the investigation of sequences and structures. J.Mol.Biol, pages 536-540, 1995.
    • (1995) J.Mol.Biol , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 22
    • 1842584503 scopus 로고    scopus 로고
    • Progressive combinatorial algorithm for multiple structural alignments: Application to distantly related proteins
    • M. E. Ochagavia and S. Wodak. Progressive combinatorial algorithm for multiple structural alignments: application to distantly related proteins. Proteins, 55:436-54, 2004.
    • (2004) Proteins , vol.55 , pp. 436-54
    • Ochagavia, M.E.1    Wodak, S.2
  • 23
    • 0036839162 scopus 로고    scopus 로고
    • Mammoth (matching molecular models obtained from theory): An automated method for model comparison
    • A. R. Ortiz, C. E. Strauss, and O. Olmea. Mammoth (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci., 11:2606-21, 2002.
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 25
    • 67649221642 scopus 로고    scopus 로고
    • Flexible structural protein alignment by a sequence of local transformations
    • J. Rocha, J. Segural, R. C. Wilson, and S. Dasgupta. Flexible structural protein alignment by a sequence of local transformations. Bioinformatics, 25(13):1625-1631, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.13 , pp. 1625-1631
    • Rocha, J.1    Segural, J.2    Wilson, R.C.3    Dasgupta, S.4
  • 26
    • 1842450688 scopus 로고    scopus 로고
    • Flexprot: Alignment of flexible protein structures without a predefinition of hinge regions
    • M. Shatsky, R. Nussinov, and H. J. Wolfson. Flexprot: alignment of flexible protein structures without a predefinition of hinge regions. J Comput Biol, 11:83-106, 2004.
    • (2004) J Comput Biol , vol.11 , pp. 83-106
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 27
    • 2442456104 scopus 로고    scopus 로고
    • A method for simultaneous alignment of multiple protein structures
    • M. Shatsky, R. Nussinov, and H. J. Wolfson. A method for simultaneous alignment of multiple protein structures. Proteins, 56:143-56, 2004.
    • (2004) Proteins , vol.56 , pp. 143-56
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 28
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (ce) of the optimal path
    • I. N. Shindyalov and P. E. Bourne. Protein structure alignment by incremental combinatorial extension (ce) of the optimal path. Protein Eng., 1:739-747, 1998.
    • (1998) Protein Eng. , vol.1 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 29
    • 0028150923 scopus 로고
    • Multiple protein structure alignment
    • W. R. Taylor, T. P. Flores, and C. A. Orengo. Multiple protein structure alignment. Protein Sci, 3:1858-70, 1994.
    • (1994) Protein Sci , vol.3 , pp. 1858-1870
    • Taylor, W.R.1    Flores, T.P.2    Orengo, C.A.3
  • 30
    • 39849110127 scopus 로고    scopus 로고
    • Sabertooth: Protein structural alignment based on a vectorial structure representation
    • F. Teichert, U. Bastolla, and M. Porto. Sabertooth: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics, 8:425, 2007.
    • (2007) BMC Bioinformatics , vol.8 , pp. 425
    • Teichert, F.1    Bastolla, U.2    Porto, M.3
  • 31
    • 19544388989 scopus 로고    scopus 로고
    • Multiple flexible structure alignment using partial order graphs
    • Y. Ye and A. Godzik. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21:2362-9, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 2362-2369
    • Ye, Y.1    Godzik, A.2
  • 32
    • 0042622381 scopus 로고    scopus 로고
    • Lga: A method for finding 3d similarities in protein structures
    • A. Zemla. Lga: A method for finding 3d similarities in protein structures. Nucleic Acids Res, 31:3370-4, 2003.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3370-334
    • Zemla, A.1
  • 33
    • 17644392830 scopus 로고    scopus 로고
    • Tm-align: A protein structure alignment algorithm based on the tm-score
    • Y. Zhang and J. Skolnick. Tm-align: a protein structure alignment algorithm based on the tm-score. Nucleic Acids Res, 33:2302-9, 2005.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2
  • 34
    • 12944271968 scopus 로고    scopus 로고
    • Fast: A novel protein structure alignment algorithm
    • J. Zhu and Z. Weng. Fast: a novel protein structure alignment algorithm. Proteins, 58:618-27, 2005.
    • (2005) Proteins , vol.58 , pp. 618-627
    • Zhu, J.1    Weng, Z.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.