Multiple Alignment of protein structures and sequences for VMD

Bioinformatics

Volumn 22, Issue 4, 2006, Pages 504-506

  Eargle, John ^a   Wright, Dan ^a   Luthey Schulten, Zaida ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 32544436601     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti825     Document Type: Article

References (12)

1. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
2. Brenner,S.E. et al. (2000) The ASTRAL compendium for sequence and structure analysis. Nucleic Acids Res., 28, 254-256.
3. Higgins,D. et al. (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, 4673-4680.
4. Humphrey,W. et al. (1996) VMD-Visual Molecular Dynamics. J. Mol. Graph., 14, 33-38.
5. Mizuguchi,K, et al. (1998) HOMSTRAD: A database of protein structure alignments for homologous families. Protein Sci., 7, 2469-2471.
6. Murzin,A.G. et al. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
7. O'Donoghue,P. and Luthey-Schulten,Z. (2003) On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol. Mol. Biol. Rev., 67, 550-573.
8. O'Donoghue,P. and Luthey-Schulten,Z. (2005) Evolutionary profiles derived from the QR factorization of multiple structural alignments gives an economy of information. J. Mol. Biol., 346, 875-894.
9. O'Donoghue,P., Sethi,A. Woese,C.R. and Luthey-Schulten,Z. (2006) The Evolutionary History of Cys-tRNA(Cys) formation. Proc. Natl. Acad. Sci. USA 102, 19003-19008.
10. Russell,R.B. and Barton,G.J. (1992) Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins, 14, 309-323.
11. Sethi,A. et al. (2005) Evolutionary profiles from the QR factorization of multiple sequence alignments. Proc. Natl Acad. Sci. USA, 102, 4045-4050.
12. Sujatha,S. et al. (2001) PALI: A database of alignments and phylogeny of homologous protein structures. Bioinformatics, 17, 375-376.