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. 2006 Jan 1;34(Database issue):D287-90.
doi: 10.1093/nar/gkj163.

E-MSD: improving data deposition and structure quality

M Tagari  1 , J Tate, G J Swaminathan, R Newman, A Naim, W Vranken, A Kapopoulou, A Hussain, J Fillon, K Henrick, S Velankar
Affiliations

E-MSD: improving data deposition and structure quality

M Tagari et al. Nucleic Acids Res. .

Abstract

The Macromolecular Structure Database (MSD) (http://www.ebi.ac.uk/msd/) [H. Boutselakis, D. Dimitropoulos, J. Fillon, A. Golovin, K. Henrick, A. Hussain, J. Ionides, M. John, P. A. Keller, E. Krissinel et al. (2003) E-MSD: the European Bioinformatics Institute Macromolecular Structure Database. Nucleic Acids Res., 31, 458-462.] group is one of the three partners in the worldwide Protein DataBank (wwPDB), the consortium entrusted with the collation, maintenance and distribution of the global repository of macromolecular structure data [H. Berman, K. Henrick and H. Nakamura (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980.]. Since its inception, the MSD group has worked with partners around the world to improve the quality of PDB data, through a clean up programme that addresses inconsistencies and inaccuracies in the legacy archive. The improvements in data quality in the legacy archive have been achieved largely through the creation of a unified data archive, in the form of a relational database that stores all of the data in the wwPDB. The three partners are working towards improving the tools and methods for the deposition of new data by the community at large. The implementation of the MSD database, together with the parallel development of improved tools and methodologies for data harvesting, validation and archival, has lead to significant improvements in the quality of data that enters the archive. Through this and related projects in the NMR and EM realms the MSD continues to improve the quality of publicly available structural data.

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References

    1. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 1994;50:760–763. - PubMed
    1. Allan R., Diakun G., Guest M., Keegan R., Nave C., Papiz M., Winn M., Winter G., Diprose J., Esnouf R., et al. Science resource for high throughput protein crystallography. Proceedings of the UK e-science All Hands Meeting. EPSRC; September 2–4; Nottingham, UK. 2003. pp. 230–234.
    1. Pajon A., Ionides J., Diprose J., Fillon J., Fogh R., Ashton A.W., Berman H., Boucher W., Cygler M., Deleury E., et al. Design of a data model for developing laboratory information management and analysis systems for protein production. Proteins. 2005;58:278–284. - PubMed
    1. Prilusky J., Oueillet E., Ulryck N., Pajon A., Bernauer J., Krimm I., Quevillon-Cheruel S., Leulliot N., Graille M., Liger D., et al. HalX: an open-source LIMS (Laboratory Information Management System) for small- to large-scale laboratories. Acta Crystallogr. D Biol. Crystallogr. 2005;61:671–678. - PubMed
    1. Morris C., Wood P., Griffiths S.L., Wilson K.S., Ashton A.W. MOLE: a data management application based on a protein production data model. Proteins. 2005;58:285–289. - PubMed

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