메뉴 건너뛰기




Volumn 40, Issue W1, 2012, Pages

CSA: Comprehensive comparison of pairwise protein structure alignments

Author keywords

[No Author keywords available]

Indexed keywords

CALMODULIN; PROTEIN;

EID: 84864493874     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks362     Document Type: Article
Times cited : (15)

References (29)
  • 1
    • 0041620359 scopus 로고    scopus 로고
    • MATRAS: A program for protein 3D structure comparison
    • Kawabata, T. (2003) MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res., 31, 3367-3369.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3367-3369
    • Kawabata, T.1
  • 2
    • 48449084095 scopus 로고    scopus 로고
    • RAPIDO: A web server for the alignment of protein structures in the presence of conformational changes
    • Mosca, R. and Schneider, T.R. (2008) RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Res., 36, 42-46.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 42-46
    • Mosca, R.1    Schneider, T.R.2
  • 3
    • 67849090550 scopus 로고    scopus 로고
    • The SALAMI protein structure search server
    • Margraf, T., Schenk, G. and Torda, A.E. (2009) The SALAMI protein structure search server. Nucleic Acids Res., 37, 480-484.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 480-484
    • Margraf, T.1    Schenk, G.2    Torda, A.E.3
  • 4
    • 77954288774 scopus 로고    scopus 로고
    • Dali server: Conservation mapping in 3D
    • Holm, L. and Rosenström, P. (2010) Dali server: conservation mapping in 3d. Nucleic Acids Res., 38, 545-549.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 545-549
    • Holm, L.1    Rosenström, P.2
  • 5
    • 66549119395 scopus 로고    scopus 로고
    • Advances and pitfalls of protein structural alignment
    • Hasegawa, H. and Holm, L. (2009) Advances and pitfalls of protein structural alignment. Curr. Opin. Struct. Biol., 19, 341-348.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 341-348
    • Hasegawa, H.1    Holm, L.2
  • 6
    • 34548304928 scopus 로고    scopus 로고
    • Comparative analysis of protein structure alignments
    • Mayr, G., Domingues, F.S. and Lackner, P. (2007) Comparative analysis of protein structure alignments. BMC Struct Biol., 7, 50-50.
    • (2007) BMC Struct Biol. , vol.7 , pp. 50-50
    • Mayr, G.1    Domingues, F.S.2    Lackner, P.3
  • 7
    • 33745596822 scopus 로고    scopus 로고
    • Integrating multiattribute similarity networks for robust representation of the protein space
    • Camoglu, O., Can, T. and Singh, A.K. (2006) Integrating multiattribute similarity networks for robust representation of the protein space. Bioinformatics, 22, 1585-1592.
    • (2006) Bioinformatics , vol.22 , pp. 1585-1592
    • Camoglu, O.1    Can, T.2    Singh, A.K.3
  • 8
    • 38949177447 scopus 로고    scopus 로고
    • Procksi: A decision support system for protein (structure) comparison, knowledge, similarity and information
    • Barthel, D., Hirst, J.D., Blazewicz, J., Burke, E.K. and Krasnogor, N. (2007) ProCKSI: a decision support system for protein (structure) comparison, knowledge, similarity and information. BMC Bioinformatics, 8, 416-416.
    • (2007) BMC Bioinformatics , vol.8 , pp. 416-416
    • Barthel, D.1    Hirst, J.D.2    Blazewicz, J.3    Burke, E.K.4    Krasnogor, N.5
  • 9
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 10
    • 0028598811 scopus 로고
    • Flexible algorithm for direct multiple alignment of protein structures and sequences
    • Godzik, A. and Skolnick, J. (1994) Flexible algorithm for direct multiple alignment of protein structures and sequences. CABIOS, 10, 587-596.
    • (1994) CABIOS , vol.10 , pp. 587-596
    • Godzik, A.1    Skolnick, J.2
  • 11
    • 0034308164 scopus 로고    scopus 로고
    • Protein structure comparison using the markov transition model of evolution
    • Kawabata, T. and Nishikawa, K. (2000) Protein structure comparison using the Markov transition model of evolution. Proteins, 41, 108-122.
    • (2000) Proteins , vol.41 , pp. 108-122
    • Kawabata, T.1    Nishikawa, K.2
  • 12
    • 77956539084 scopus 로고    scopus 로고
    • Towards optimal alignment of protein structure distance matrices
    • Wohlers, I., Domingues, F.S. and Klau, G.W. (2010) Towards optimal alignment of protein structure distance matrices. Bioinformatics, 26, 2273-2280.
    • (2010) Bioinformatics , vol.26 , pp. 2273-2280
    • Wohlers, I.1    Domingues, F.S.2    Klau, G.W.3
  • 14
    • 79960116362 scopus 로고    scopus 로고
    • Algorithm engineering for optimal alignment of protein structure distance matrices
    • Wohlers, I., Andonov, R. and Klau, G.W. (2011) Algorithm engineering for optimal alignment of protein structure distance matrices. Optimization Lett., 5, 421-433.
    • (2011) Optimization Lett. , vol.5 , pp. 421-433
    • Wohlers, I.1    Andonov, R.2    Klau, G.W.3
  • 16
    • 0344033635 scopus 로고    scopus 로고
    • PDB file parser and structure class implemented in python
    • Hamelryck, T. and Manderick, B. (2003) PDB file parser and structure class implemented in python. Bioinformatics, 19, 2308-2310.
    • (2003) Bioinformatics , vol.19 , pp. 2308-2310
    • Hamelryck, T.1    Manderick, B.2
  • 17
    • 70349464982 scopus 로고    scopus 로고
    • Accuracy analysis of multiple structure alignments
    • Berbalk, C., Schwaiger, C.S. and Lackner, P. (2009) Accuracy analysis of multiple structure alignments. Protein Sci., 18, 2027-2035.
    • (2009) Protein Sci. , vol.18 , pp. 2027-2035
    • Berbalk, C.1    Schwaiger, C.S.2    Lackner, P.3
  • 18
    • 33846074754 scopus 로고    scopus 로고
    • SISYPHUS-structural alignments for proteins with non-trivial relationships
    • Andreeva, A., PrlićA., Hubbard, T.J. and Murzin, A.G. (2007) SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res., 35, 253-259.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 253-259
    • Andreeva, A.1    Prlić, A.2    Hubbard, T.J.3    Murzin, A.G.4
  • 20
    • 27544448536 scopus 로고    scopus 로고
    • Implementing the ihop concept for navigation of biomedical literature
    • Hoffmann, R. and Valencia, A. (2005) Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics, 21(Suppl. 2), 252-258.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2 , pp. 252-258
    • Hoffmann, R.1    Valencia, A.2
  • 21
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and 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
  • 22
    • 0345616428 scopus 로고    scopus 로고
    • A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain
    • Shih, S.C., Prag, G., Francis, S.A., Sutanto, M.A., Hurley, J.H. and Hicke, L. (2003) A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain. EMBO J., 22, 1273-1281.
    • (2003) EMBO J. , vol.22 , pp. 1273-1281
    • Shih, S.C.1    Prag, G.2    Francis, S.A.3    Sutanto, M.A.4    Hurley, J.H.5    Hicke, L.6
  • 23
    • 0032189646 scopus 로고    scopus 로고
    • Dictionary of recurrent domains in protein structures
    • Holm, L. and Sander, C. (1998) Dictionary of recurrent domains in protein structures. Proteins, 33, 88-96.
    • (1998) Proteins , vol.33 , pp. 88-96
    • Holm, L.1    Sander, C.2
  • 24
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Zhang, Y. and Skolnick, J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins, 57, 702-710.
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 25
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • Carugo, O. and Pongor, S. (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci., 10, 1470-1473.
    • (2001) Protein Sci. , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 26
    • 0029982530 scopus 로고    scopus 로고
    • The structural alignment between two proteins: Is there a unique answer?
    • Godzik, A. (1996) The structural alignment between two proteins: is there a unique answer? Protein Sci., 5, 1325-1338.
    • (1996) Protein Sci. , vol.5 , pp. 1325-1338
    • Godzik, A.1
  • 27
    • 17644392830 scopus 로고    scopus 로고
    • Tm-align: A protein structure alignment algorithm based on the tm-score
    • Zhang, Y. and Skolnick, J. (2005) Tm-align: a protein structure alignment algorithm based on the tm-score. Nucleic Acids Res, 33, 2302-2309.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.