3did: Interacting protein domains of known three-dimensional structure

Nucleic Acids Research

Volumn 33, Issue DATABASE ISS., 2005, Pages

  Stein, Amelie ^a   Russell, Robert B ^a,b   Aloy, Patrick ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

3D INTERACTING DOMAINS; COMPUTER PROGRAM; GENE FUNCTION; GENE INTERACTION; GENE ONTOLOGY; GENETIC DATABASE; INFORMATION PROCESSING; INTERNET; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; REVIEW; YEAST; 3D INTERACTING DOMAINS DATABASE; ARTICLE; MOLECULAR DYNAMICS; PROTEIN INTERACTION; SACCHAROMYCES CEREVISIAE;

DATABASES, PROTEIN; FUNGAL PROTEINS; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, TERTIARY; PROTEINS; USER-COMPUTER INTERFACE;

SACCHAROMYCES CEREVISIAE;

EID: 13444257903     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki037     Document Type: Review

References (19)

1. Uetz,P., Giot,L., Cagney,G., Mansfield,T.A., Judson,R.S., Knight,J.R., Lockshon,D., Narayan,V., Srinivasan,M., Pochart,P. et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature, 403, 623-627.
2. Ito,T., Chiba,T., Ozawa,R., Yoshida,M., Hattori,M. and Sakaki,Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl Acad. Sci. USA, 98, 4569-4574.
3. Rain,J.C., Selig,L., De Reuse,H., Battaglia,V., Reverdy,C., Simon,S., Lenzen,G., Petel, F., Wojcik,J., Schachter,V. et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature, 409, 211-215.
4. 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.
5. 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.
6. 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.
7. 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.
8. 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.
9. Bourne,P.E., Addess,K.J., Bluhm,W.F., Chen,L., Deshpande,N., Feng,Z., Fleri,W., Green,R., Merino-Ott,J.C., Townsend-Merino,W. et al. (2004) The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res., 32, D223-D225.
10. 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, D138-D141.
11. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene Ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genet., 25, 25-29.
12. Mewes,H.W., Amid,C., Arnold,R., Frishman,D., Guldener,U., Mannhaupt,G., Munsterkotter,M., Pagel,P., Strack,N., Stumpflen,V. et al. (2004) MIPS: analysis and annotation of proteins from whole genomes. Nucleic Acids Res., 32, D41-D44.
13. Aloy,P. and Russell,R.B. (2002) Interrogating protein interaction networks through structural biology. Proc. Natl Acad. Sci. USA, 99, 5896-5901.
14. Aloy,P. and Russell,R.B. (2003) InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics, 19, 161-162.
15. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all Trends Biochem. Sci., 20, 374.
16. Aloy,P., Ceulemans,H., Stark,A. and Russell,R.B. (2003) The relationship between sequence and interaction divergence in proteins. J. Mol. Biol., 332, 989-998.
17. Andreeva,A., Howorth,D., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res., 32, D226-D229.
18. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
19. Letunic,I., Copley,R.R., Schmidt,S., Ciccarelli,F.D., Doerks,T., Schultz,J., Ponting,C.P. and Bork,P. (2004) SMART 4.0: towards genomic data integration Nucleic Acids Res., 32, D142-D144.