PCOAT: Positional correlation analysis using multiple methods

Bioinformatics

Volumn 20, Issue 18, 2004, Pages 3697-3699

  Qi, Yuan ^b   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS AT DALLAS   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; CORRELATION ANALYSIS; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SAMPLING; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICS;

EID: 12344256786     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth431     Document Type: Article

References (15)

1. Afonnikov,D.A., Oshchepkov,D.Y. and Kolchanov,N.A. (2001) Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics, 17, 1035-1046.
2. Atchley,W.R., Wollenberg,K.R., Fitch,W.M., Terhalle,W. and Dress, A.W. (2000) Correlations among amino acid sites in bHLH protein domains: an information theoretic analysis. Mol. Biol. Evol., 17 164-178.
3. Bateman,A., Coin,L., Durbin,R., Finn,R.D., Hollich,V., Griffiths-Jones,S., Khanna,A., Marshall,M., Moxon,S., Sonnhammer,E.L. et al. (2004) The Pfam protein families database. Nucleic Acids Res., 32 (Database issue) D138-D141.
4. Crowder,S., Holton,J. and Alber,T. (2001) Covariance analysis of RNA recognition motifs identifies functionally linked amino acids. J. Mol. Biol., 310, 793-800.
5. Henikoff,S. and Henikoff,J.G. (1994) Position-based sequence weights. J. Mol. Biol., 243, 574-578.
6. Iuchi,S. (2001) Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci., 58, 625-635.
7. Kobe,B., Jennings,I.G., House,C.M., Michell,B.J., Goodwill,K.E., Santarsiero,B.D., Stevens,R.C., Cotton,R.G. and Kemp,B.E. (1999) Structural basis of autoregulation of phenylalanine hydroxylase. Nat. Struct. Biol., 6, 442-448.
8. Larson,S.M., Di Nardo,A.A. and Davidson,A.R. (2000) Analysis of covariation in an SH3 domain sequence alignment: applications in tertiary contact prediction and the design of compensating hydrophobic core substitutions. J. Mol. Biol., 303, 433-446.
9. Mateu,M.G. and Fersht,A.R. (1999) Mutually compensatory mutations during evolution of the tetramerization domain of tumor suppressor p53 lead to impaired hetero-oligomerization. Proc. Natl Acad. Sci., USA, 96, 3595-3599.
10. Pei,J. and Grishin,N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712.
11. Pollock,D.D. and Taylor,W.R. (1997) Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng., 10, 647-657.
12. Saraf,M.C., Moore,G.L. and Maranas,C.D. (2003) Using multiple sequence correlation analysis to characterize functionally important protein regions. Protein Eng., 16, 397-406.
13. Suel,G.M., Lockless,S.W., Wall,M.A. and Ranganathan,R. (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat. Struct. Biol., 10, 59-69.
14. Sunyaev,S.R., Eisenhaber,F., Rodchenkov,I.V., Eisenhaber,B., Tumanyan,V.G. and Kuznetsov,E.N. (1999) PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. Protein Eng., 12, 387-394.
15. Tillier,E.R. and Lui,T.W. (2003) Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Bioinformatics, 19, 750-755.