Protein structure alignment considering phenotypic plasticity

Bioinformatics

Volumn 24, Issue 16, 2008, Pages

  Csaba, Gergely ^a   Birzele, Fabian ^a   Zimmer, Ralf ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; CLASSIFICATION; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; INTERMETHOD COMPARISON; LINEAR SYSTEM; MATHEMATICAL COMPUTING; PHENOTYPIC PLASTICITY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SEQUENCE HOMOLOGY;

EID: 49549085536     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn271     Document Type: Conference Paper

References (15)

1. Andreeva,A. et al. (2007) Data growth and its impact on the scop database: New developments. Nucleic Acids Res., 36(Database issue), D419-D425.
2. Berman,H. et al. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
3. Birzele,F. et al. (2007) Vorolign-fast structural alignment using Voronoi contacts. Bioinformatics, 23, e205-e211.
4. Birzele,F. et al. (2008) Alternative splicing and protein structure evolution. Nucleic Acids Res., 36, 550-558.
5. Dayhoff,M.O. et al. (1978) A model of evolutionary change in proteins. Atlas of Protein Sequence and Structure, 5, 345-352.
6. Grabowski,M. et al. (2007) Structural genomics: Keeping up with expanding knowledge of the protein universe. Curr. Opin. Struct. Biol., 17, 347-353.
7. Greene,L.H. et al. (2007) The cath domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res., 35(Database issue), D291-D297.
8. Hadley,C. and Jones,D. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure, 7 1099-1112.
9. Harrison,A. et al. (2003) Recognizing the fold of a protein structure. Bioinformatics, 19, 1748-1759.
10. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
11. 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.
12. von Ohsen,N. et al. (2003) Profile-profile alignment: A powerful tool for protein structure prediction. Pac. Symp. Biocomput., 252-263.
13. Ye,Y. and Godzik,A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics., 19 (Suppl. 2), II246-II255.
14. Zhang,Y. and Skolnick,J. (2004) Scoring function for automated assessment of protein structure template quality. Proteins. 57 702-710.
15. Zhang,Y. and Skolnick,J. (2005) TM-align: A protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 33, 2302-2309.