D364 Nucleic Acids Research, 2009, Vol. 37, Database issue Scientiﬁc Research on Priority Areas from the Ministry of Education, Culture, Sports, Science and Technology of Japan (to K.K.). Funding for open access charge: Annual budget for Human Genome Center. Conﬂict of interest statement. None declared. REFERENCES 1. 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. 2. Chandonia,J.M. and Brenner,S.E. (2006) The impact of structural genomics: expectations and outcomes. Science, 311, 347–351. 3. Koike,R., Amemiya,T., Ota,M. and Kidera,A. (2008) Protein structural change upon ligand binding correlates with enzymatic reaction mechanism. J. Mol. Biol., 379, 397–401. 4. Levy,E.D., Boeri Erba,E., Robinson,C.V. and Teichmann,S.A. (2008) Assembly reﬂects evolution of protein complexes. Nature, 453, 1262–1265. 5. Levy,E.D., Pereira-Leal,J.B., Chothia,C. and Teichmann,S.A. (2006) 3D complex: a structural classiﬁcation of protein complexes. PLoS Comp. Biol., 2, e155. 6. Higurashi,M., Ishida,T. and Kinoshita,K. (2008) Identiﬁcation of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci., 17, 72–78. 7. Jones,S. and Thornton,J.M. (1995) Protein-protein interactions: a review of protein dimer structures. Prog. Biophys. Mol. Biol., 63, 31–65. 8. Keskin,O., Gursoy,A., Ma,B. and Nussinov,R. (2008) ) Principles of Protein-protein interactions: what are the preferred ways for pro- teins to interact? Chem. Rev., 108, 1225–1244. 9. Huang,B. and Schroeder,M. (2008) Using protein binding site pre- diction to improve protein docking. Gene, 422, 14–21. 10. Zhou,H.-X. and Qin,S. (2007) Interaction-site prediction for protein complexes: a critical assessment. Bioinformatics, 23, 2203–2209. 11. Valdar,W.S. and Thornton,J.M. (2001) Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins, 42, 108–124. 12. Bahadur,R.P., Chakrabarti,P., Rodier,F. and Janin,J. (2004) A dissection of speciﬁc and non-speciﬁc protein-protein interfaces. J. Mol. Biol., 336, 943–955. 13. Jeong,H., Mason,S.P., Barabasi,A.L. and Oltvai,Z.N. (2001) Lethality and centrality in protein networks. Nature, 411, 41–42. 14. Kim,W., Bolser,D. and Park,J. (2004) Large-scale co-evolution analysis of protein structural interlogues using the global protein structural interactome map (PSIMAP). Bioinformatics, 20, 1138–1150. 15. Stein,A., Russell,R.B. and Aloy,P. (2005) 3did: interacting protein domains of known three-dimensional structure. Nucleic Acid Res., 33, D413–D417. 16. Raghavachari,B., Tasneem,A., Przytycka,T.M. and Jothi,R. (2007) DOMINE: a database of protein domain interactions. Nucleic Acids Res., 36, 656–661. 17. Winter,C., Henschel,A., Kim,W.K. and Schroeder,M. (2006) SCOPPI: a structural classiﬁcation of protein-protein interfaces. Nucleic Acids Res., 34, D310–D314. 18. Finn,R., Marshall,M. and Bateman,A. (2005) iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21, 410–412. 19. Davis,F.P. and Sali,A. (2005) PIBASE: a comprehensive database of structurally deﬁned protein interfaces. Bioinformatics, 21, 1901–1907. 20. 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. 21. 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 interac- tions in Saccharomyces cerevisiae. Nature, 403, 623–627. 22. 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. 23. 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. 24. 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. 25. UnitProt Consortium. (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190–D195. 26. Kinoshita,K. and Nakamura,H. (2004) eF-site and PDBjViewer: database and viewer for protein functional sites. Bioinformatics, 20, 1329–1330. 27. Sigal,I.S., Gibbs,J.B., D’Alonzo,J.S. and Scolnick,E.M. (1986) Identiﬁcation of eﬀector residues and a neutralizing epitope of Ha-ras-encoded p21. Proc. Natl Acad. Sci. USA, 83, 4725–4729.