ADVICE: Automated detection and validation of interaction by Co-evolution

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Tan, Soon Heng ^a   Zhang, Zhuo ^a   Ng, See Kiong ^a  

^a INSTITUTE FOR INFOCOMM RESEARCH   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; INTERNET; METHODOLOGY; MOLECULAR EVOLUTION; ORTHOLOGY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

EVOLUTION, MOLECULAR; INTERNET; PROTEIN INTERACTION MAPPING; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 3242892063     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh471     Document Type: Article

References (20)

1. Fraser,H.B., Hirsh,A.E., Steinmetz,L.M., Scharfe,C. and Feldman,M.W. (2002) Evolutionary rate in the protein interaction network. Science, 296, 750-752.
2. Moyle,W.R., Campbell,R.K., Myers,R.V., Bernard,M.P., Han,Y. and Wang,X. (1994) Co-evolution of ligand-receptor pairs. Nature, 368, 251-255.
3. van Kesteren,R.E., Tensen,C.P., Smit,A.B., van Minnen,J., Kolakowski,L.F., Meyerhof,W., Richter,D., van Heerikhuizen,H., Vreugdenhil,E. and Geraerts,W.P. (1996) Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides. J. Biol. Chem., 271, 3619-3626.
4. Hughes,A.L. and Yeager,M. (1999) Coevolution of the mammalian chemokines and their receptors. Immunogenetics, 49, 115-124.
5. Koretke,K.K., Lupas,A.N., Warren,P.V., Rosenberg,M. and Brown,J.R. (2000) Evolution of two-component signal transduction. Mol. Biol. Evol., 17, 1956-1970.
6. Pazos,F., Helmer-Citterich,M., Ausiello,G. and Valencia,A. (1997) Correlated mutations contain information about protein-protein interaction. J. Mol. Biol., 271, 511-523.
7. Jespers,L., Lijnen,H.R., Vanwetswinkel,S., Van Hoef,B., Brepoels,K., Collen,D. and De Maeyer,M. (1999) Guiding a docking mode by phage display: selection of correlated mutations at the staphylokinase-plasmin interface. J. Mol. Biol., 290, 471-479.
8. Jucovic,M. and Hartley,R.W. (1996) Protein-protein interaction: a genetic selection for compensating mutations at the barnase-barstar interface. Proc. Natl Acad. Sci. USA, 93, 2343-2347.
9. Goh,C.S., Bogan,A.A., Joachimiak,M., Walther,D. and Cohen,F.E. (2000) Co-evolution of proteins with their interaction partners. J. Mol. Biol., 299, 283-293.
10. Pazos,F. and Valencia,A. (2001) Similarity of phylogenetic trees as indicator of protein-protein interaction. Protein Eng., 14, 609-614.
11. Ramani,A.K. and Marcotte,E.M. (2003) Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol., 327, 273-284.
12. Giot,L., Bader,J.S., Brouwer,C., Chaudhuri,A., Kuang,B., Li,Y., Hao,Y.L., Ooi,C.E., Godwin,B., Vitols,E. et al. (2003) A protein interaction map of Drosophila melanogaster. Science, 302, 1727-1736.
13. Li,S., Armstrong,C.M., Bertin,N., Ge,H., Milstein,S., Boxem,M., Vidalain,P.O., Han,J.D., Chesneau,A., Hao,T. et al. (2004) A map of the interactome network of the metazoan C.elegans. Science, 303, 540-543.
14. Ho,Y., Gruhler,A., Heilbut,A., Bader,G.D., Moore,L., Adams,S.L., Millar,A., Taylor,P., Bennett,K., Boutilier,K. et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature, 415, 180-183.
15. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141-147.
16. Zhu,H., Bilgin,M., Bangham,R., Hall,D., Casamayor,A., Bertone,P., Lan,N., Jansen,R., Bidlingmaier,S., Houfek,T. et al. (2001) Global analysis of protein activities using proteome chips. Science, 293, 2101-2105.
17. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
18. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
19. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (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.
20. von Mering,C., Krause,R., Snel,B., Cornell,M., Oliver,S.G., Fields,S. and Bork,P. (2002) Comparative assessment of large-scale data sets of protein-protein interactions. Nature, 417, 399-403.