ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information

Bioinformatics

Volumn 19, Issue 1, 2003, Pages 163-164

  Glaser, Fabian ^a   Pupko, Tal ^b   Paz, Inbal ^a   Bell, Rachel E ^a   Bechor Shental, Dalit ^a   Martz, Eric ^c   Ben Tal, Nir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN; PROTEIN BCL XL;

ALGORITHM; ARTICLE; AUTOMATION; COMPUTER PROGRAM; GENE MAPPING; GENETIC CONSERVATION; MOLECULAR PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN FUNCTION; SEQUENCE HOMOLOGY; THREE DIMENSIONAL IMAGING;

EID: 2542445427     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/19.1.163     Document Type: Article

References (14)

1. Adams,J.M. and Cory,S. (1998) The Bcl-2 protein family: arbiters of cell survival. Science, 281, 1322-1326.
2. Aloy,P., Querol,E., Aviles,F.X. and Sternberg,M.J. (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408.
3. Armon,A., Graur,D. and Ben-Tal,N. (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol., 367, 447-463.
4. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N., Weissig,H., Shindyalov,I.N. and Bourne,P.E. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
5. Brenner,S.E. (2001) A tour of structural genomics. Nat. Rev. Genet., 2, 801-809.
6. Innis,C.A., Shi,J. and Blundell,T.L. (2000) Evolutionary trace analysis of TGF-beta and related growth factors: implications for site-directed mutagenesis. Protein Eng., 13, 839-847.
7. Landgraf,R., Xenarios,I. and Eisenberg,D. (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 307, 1487-1502.
8. Lichtarge,O., Bourne,H.R. and Cohen,F.E. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
9. Martz,E. (2002) Protein explorer: easy yet powerful macromolecular visualization. Trends Biochem. Sci, 27, 107-109.
10. Pupko,T., Bell,R.E., Mayrose,I., Glaser,F. and Ben-Tal,N. (2002) Rate4Site: An algorithmic tool for the identification of functional regions on proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18 (suppl), S71-S77.
11. Sattler,M., Liang,H., Nettesheim,D., Meadows,R.P., Harlan,J.E., Eberstadt,M., Yoon,H.S., Shuker,S.B., Chang,B.S., Minn,A.J., Thompson,C.B. and Fesik,S.W. (1997) Structure of Bcl-xL-Bak peptide complex: recognition between regulators of apoptosis. Science, 275, 983-986.
12. Schneider,R. and Sander,C. (1996) The HSSP database of protein structure-sequence alignments. Nucleic Acids Res., 24, 201-205.
13. Valdar,W.S. and Thornton,J.M. (2001) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins, 42, 108-124.
14. Yona,G., Linial,N. and Linial,M. (2000) ProtoMap: automatic classification of protein sequences and hierarchy of protein families. Nucleic Acids Res., 28, 49-55.