The iRMSD: A local measure of sequence alignment accuracy using structural information

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Armougom, Fabrice ^a   Moretti, Sébastien ^a   Keduas, Vladimir ^a   Notredame, Cedric ^a  

^a CNRS Aix Marseille University   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; BIOINFORMATICS; COMPUTER PROGRAM; CONFERENCE PAPER; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ALIGNMENT;

EID: 33747877691     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl218     Document Type: Conference Paper

References (22)

1. Do,C.B., Mahabhashyam,M.S., Brudno,M. and Batzoglou,S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res, 15, 330-340.
2. Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res, 32, 1792-1797. Print 2004.
3. Goldsmith-Fischman,S. and Honig,B. (2003) Structural genomics: computational methods for structure analysis. Protein Sci, 12, 1813-1821.
4. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol, 233, 123-138.
5. Huang,Y.M. and Bystroff,C. (2006) Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics, 22, 413-422.
6. Katoh,K., Kuma,K., Toh,H. and Miyata,T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res, 33, 511-518.
7. Kleywegt,G.J. and Jones,T.A. (1994) Superposition. CCP4/ESF-EACBM Newsletter Protein Crystallog., 31, 9-14.
8. Kleywegt,G.J. and Jones,T.A. (1999) Software for handling macromolecular envelopes. Acta Crystallogr D Biol Crystallogr, 55 (Pt 4), 941-944.
9. Kolodny,R., Koehl,P. and Levitt,M. (2005) Comprehensive evaluation of protein structure alignment methods: Scoring by geometric measures. J Mol Biol, 346, 1173-1188.
10. Lackner,P., Koppensteiner,W.A., Sippl,M.J. and Domingues,F.S. (2000) ProSup: A refined tool for protein structure alignment. Protein Eng, 13, 745-752.
11. Lesk,A.M. and Chothia,C. (1980) How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins. J Mol Biol, 136, 225-270.
12. Mizuguchi,K., Deane,C.M., Blundell,T.L. and Overington,J.P. (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci, 7, 2469-2471.
13. Morgenstern,B. (1999) DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment [In Process Citation]. Bioinformatics, 15, 211-218.
14. Notredame,C., Higgins,D.G. and Heringa,J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol, 302, 205-217.
15. O'Sullivan,O., Suhre,K., Abergel,C., Higgins,D.G. and Notredame,C. (2004) 3DCoffee: Combining protein sequences and structures within multiple sequence alignments. J Mol Biol, 340, 385-395.
16. O'Sullivan,O., Zehnder,M., Higgins,D., Bucher,P., Grosdidier,A. and Notredame,C. (2003) APDB: A novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics, 19 Suppl 1, i215-221.
17. Raghava,G.P., Searle,S.M., Audley,P.C., Barber,J.D. and Barton,G.J. (2003) OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracy. BMC Bioinformatics, 4, 47.
18. 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.
19. Thompson,J., Higgins,D. and Gibson,T. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4690.
20. Thompson,J.D., Koehl,P., Ripp,R. and Poch,O. (2005) BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
21. Van Walle,I., Lasters,I. and Wyns,L. (2005) SABmark - a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics, 21, 1267-1268.
22. Wallace,I.M., Blackshields,G. and Higgins,D.G. (2005) Multiple sequence alignments. Curr Opin Struct Biol, 15, 261-266.