D290 Nucleic Acids Research, 2006, Vol. 34, Database issue Funding to pay the Open Access publication charges for this article was provided by The Wellcome Trust. Conflict of interest statement. None declared. REFERENCES 1. Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr., 50, 760–763. 2. Allan,R., Diakun,G., Guest,M., Keegan,R., Nave,C., Papiz,M., Winn,M., Winter,G., Diprose,J., Esnouf,R. et al. (2003) Science resource for high throughput protein crystallography. Proceedings of the UK e-science All Hands Meeting. EPSRC, September 2–4, Nottingham, UK , pp. 230–234. 3. Pajon,A., Ionides,J., Diprose,J., Fillon,J., Fogh,R., Ashton,A.W., Berman,H., Boucher,W., Cygler,M., Deleury,E. et al. (2005) Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins, 58, 278–284. 4. Prilusky,J., Oueillet,E., Ulryck,N., Pajon,A., Bernauer,J., Krimm,I., Quevillon-Cheruel,S., Leulliot,N., Graille,M., Liger,D. et al. (2005) HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr. D Biol. Crystallogr., 61, 671–678. 5. Morris,C., Wood,P., Griffiths,S.L., Wilson,K.S. and Ashton,A.W. (2005) MOLE: a data management application based on a protein production data model. Proteins, 58, 285–289. 6. Vranken,W.F., Boucher,W., Stevens,T.J., Fogh,R.H., Pajon,A., Llinas,M., Ulrich,E.L., Markley,J.L., Ionides,J. and Laue,E.D. (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins, 59, 687–696. 7. Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358–361. 8. Kleywegt,G.J., Harris,M.R., Zou,J.Y., Taylor,T.C., Wahlby,A. and Jones,T.A. (2004) The Uppsala Electron-Density Server. Acta Crystallogr. D Biol. Crystallogr., 60, 2240–2249. 9. Vaguine,A.A., Richelle,J. and Wodak,S.J. (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure- factor data and their agreement with the atomic model. Acta Crystallogr. D Biol. Crystallogr., 55, 191–205. 10. Apweiler,R., Bairoch,A., Wu,C.H., Barker,W.C., Boeckmann,B., Ferro,S., Gasteiger,E., Huang,H., Lopez,R., Magrane,M. et al. (2004) UniProt: the Universal Protein knowledgebase. Nucleic Acids Res., 32, D115–D119. 11. Velankar,S., McNeil,P., Mittard-Runte,V., Suarez,A., Barrell,D., Apweiler,R. and Henrick,K. (2005) E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res., 33, D262–D265. 12. Krissinel,E. and Henrick,K. (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr., 60, 2256–2268. 13. Tagari,M., Newman,R., Chagoyen,M., Carazo,J.M. and Henrick,K. (2002) New electron microscopy database and deposition system. Trends Biochem. Sci., 27, 589. 14. Henrick,K., Newman,R., Tagari,M. and Chagoyen,M. (2003) EMDep: a web-based system for the deposition and validation of high-resolution electron microscopy macromolecular structural information. J. Struct. Biol., 144, 228–237. 15. Camon,E., Magrane,M., Barrell,D., Lee,V., Dimmer,E., Maslen,J., Binns,D., Harte,N., Lopez,R. and Apweiler,R. (2004) The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res., 32, D262–D266. 16. Mulder,N.J., Apweiler,R., Attwood,T.K., Bairoch,A., Barrell,D., Bateman,A., Binns,D., Biswas,M., Bradley,P., Bork,P. et al. (2003) The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res., 31, 315–318. 17. Fuller,S.D. (2003) Depositing electron microscopy maps. Structure (Camb.), 11, 11–12. 18. Fogh,R., Ionides,J., Ulrich,E., Boucher,W., Vranken,W., Linge,J.P., Habeck,M., Rieping,W., Bhat,T.N., Westbrook,J. et al. (2002) The CCPN project: an interim report on a data model for the NMR community. Nature Struct. Biol., 9, 416–418. 19. Fogh,R.H., Boucher,W., Vranken,W.F., Pajon,A., Stevens,T.J., Bhat,T.N., Westbrook,J., Ionides,J.M. and Laue,E.D. (2005) A framework for scientific data modeling and automated software development. Bioinformatics, 21, 1678–1684. 20. Doreleijers,J.F., Rullmann,J.A. and Kaptein,R. (1998) Quality assessment of NMR structures: a statistical survey. J. Mol. Biol., 281, 149–164. 21. Nederveen,A.J., Doreleijers,J.F., Vranken,W., Miller,Z., Spronk,C.A., Nabuurs,S.B., Guntert,P., Livny,M., Markley,J.L., Nilges,M. et al. (2005) RECOORD: a recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank. Proteins, 59, 662–672. 22. Doreleijers,J.F., Nederveen,A.J., Vranken,W., Lin,J., Bonvin,A.M., Kaptein,R., Markley,J.L. and Ulrich,E.L. (2005) BioMagResBank databases DOCR and FRED containing converted and filtered sets of experimental NMR restraints and coordinates from over 500 protein PDB structures. J. Biomol. NMR, 32, 1–12.