Nucleic Acids Research, 2012, Vol. 40, Database issue D557 Figure 3. An example of a web page: hypothetical oxidoreductase YIAK (32). The numbers indicate the PSCID and protein name [1], PDB box [2], protein and ligand structures [3], animation button [4], PNG image button [5], function box [6], ligand box [7] and segment box [8]. entries are deposited. A liaison to the BLAST (36) homology search program will also be available. ACKNOWLEDGEMENTS The authors are grateful to Kiyotaka Misoo and Natsuko Hama for their contributions to the website design. FUNDING Funding for open access charge: Ministry of Education, Culture, Sports, Science and Technology of Japan. Conﬂict of interest statement. None declared. REFERENCES 1. Bernstein,F.C., Koetzle,T.F., Williams,G.J., Meyer,E.F. Jr, Brice,M.D., Rodgers,J.R., Kennard,O., Shimanouchi,T. and Tasumi,M. (1977) The Protein Data Bank: a computer-based archival ﬁle for macromolecular structures. J. Mol. Biol., 112, 535–542. 2. Rose,P.W., Beran,B., Bi,C., Bluhm,W.F., Dimitropoulos,D., Goodsell,D.S., Prlic´ ,A., Quesada,M., Quinn,G.B., Westbrook,J.D. et al. (2010) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392–D401. 3. Tama,F. and Sanejouand,Y.H. (2001) Conformational change of proteins arising from normal mode calculations. Protein Eng., 14, 1–6. 4. Hammes,G.G. (2002) Multiple conformational changes in enzyme catalysis. Biochemistry, 41, 8221–8228. 5. Hayward,S. (2004) Identiﬁcation of speciﬁc interactions that drive ligand-induced closure in ﬁve enzymes with classic domain movements. J. Mol. Biol., 339, 1001–1021. 6. Gutteridge,A. and Thornton,J. (2004) Conformational change in substrate binding, catalysis and product release: an open and shut case? FEBS Lett., 567, 67–73. 7. Gutteridge,A. and Thornton,J. (2005) Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol., 346, 21–28. 8. Alexandrov,V., Lehnert,U., Echols,N., Milburn,D., Engelman,D. and Gerstein,M. (2005) Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool. Protein Sci., 14, 633–643. 9. Gunasekaran,K. and Nussinov,R. (2007) How different are structurally ﬂexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J. Mol. Biol., 365, 257–273. 10. Keskin,O. (2007) Binding induced conformational changes of proteins correlate with their intrinsic ﬂuctuations: a case study of antibodies. BMC Struct. Biol., 7, 1–11. 11. Yang,L., Song,G. and Jernigan,R.L. (2007) How well can we understand large-scale proteins motions using normal modes of elastic network models. Biophys. J., 93, 920–929.