Pre-calculated protein structure alignments at the RCSB PDB website

Bioinformatics

Volumn 26, Issue 23, 2010, Pages 2983-2985

  Prlić, Andreas ^a   Bliven, Spencer ^b   Rose, Peter W ^a   Bluhm, Wolfgang F ^a   Bizon, Chris ^c   Godzik, Adam ^b   Bourne, Philip E ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF NORTH CAROLINA   (United States)

^d UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; INTERNET; PROTEIN DATABASE; STRUCTURAL HOMOLOGY;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; INTERNET; PROTEINS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

EID: 78449284386     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq572     Document Type: Article

References (22)

1. Alden, K. et al. (2010) dconsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment. BMC Bioinformatics, 11, 310.
2. Altschul et al. (2004) BLASTClust. Available at: http://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html (last accessed date October 20, 2010).
3. Andreeva, A. et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425.
4. Andreeva, A. et al. (2006) SISYPHUS-structural alignments for proteins with non-trivial relationships. Nucleic Acids Res., 35, D253-D259.
5. Bachar, O. et al. (1993)Acomputer vision based technique for 3-d sequence-independent structural comparison of proteins. Protein Eng., 6, 279-288.
6. Berman, H.M. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
7. Cuff, A. et al. (2009) The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure, 17, 1051-1062.
8. Holland, R.C.G. et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics, 24, 2096-2097.
9. Holm, L. and Sander, C. (1993) Protein structure comparison by alignment of distance matrices. J.Mol.Biol., 233, 123-138.
10. Jmol (2010) Jmol: an open-source Java viewer for chemical structures in 3D. Available at: http://www.jmol.org/ (last accessed date October 20, 2010).
11. Needleman, S.B. andWunsch, C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequences of two proteins. J. Mol. Biol., 48, 443-453.
12. Nussinov, R. andWolfson, H.J. (1991) Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA, 88, 10495-10499.
13. Ortiz, A.R. et al. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison. Protein Sci, 11, 2606-2621.
14. Shindyalov, I.N. and Bourne, P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
15. Sippl, M.J. (2008) On distance and similarity in fold space. Bioinformatics, 24, 872-873.
16. Sippl, M.J. andWiederstein, M. (2008)Anote on difficult structure alignment problems. Bioinformatics, 24, 426-427.
17. Smith, T.F. and Waterman, M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
18. Tatusova, T.A. and Madden, T.L. (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett., 174, 247-250.
19. Veeramalai, M. et al. (2008) TOPS++FATCAT: fast flexible structural alignment using constraints derived from TOPS+ Strings Model. BMC Bioinformatics, 9, 358.
20. Ye, Y. and Godzik, A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics, 19(Suppl. 2), II246-II255.
21. Ye, Y. and Godzik, A. (2004) FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res., 32, W582-W585.
22. Zhang, Y. and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.