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. 2005 Jan 1;33(Database issue):D262-5.
doi: 10.1093/nar/gki058.

E-MSD: an integrated data resource for bioinformatics

S Velankar  1 , P McNeil, V Mittard-Runte, A Suarez, D Barrell, R Apweiler, K Henrick
Affiliations

E-MSD: an integrated data resource for bioinformatics

S Velankar et al. Nucleic Acids Res. .

Abstract

The Macromolecular Structure Database (MSD) group (http://www.ebi.ac.uk/msd/) continues to enhance the quality and consistency of macromolecular structure data in the worldwide Protein Data Bank (wwPDB) and to work towards the integration of various bioinformatics data resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. This information is vital for the reliable integration of the sequence family databases such as Pfam and Interpro with the structure-oriented databases of SCOP and CATH. This information has been made available to the eFamily group (http://www.efamily.org.uk/) and now forms the basis of the regular interchange of information between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH). This exchange of annotation information has enriched the structural information in the MSD database with annotation from wider sequence-oriented resources. This work was carried out under the 'Structure Integration with Function, Taxonomy and Sequences (SIFTS)' initiative (http://www.ebi.ac.uk/msd-srv/docs/sifts) in the MSD group.

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Figures

Figure 1
Figure 1
The database schema supporting the MSD to UniProt residue-level mapping. MSD components are in white, external database components in yellow and the cross-reference components in green.
See this image and copyright information in PMC

References

    1. Kulikova T., Aldebert,P., Althorpe,N., Baker,W., Bates,K., Browne,P., van den Broek,A., Cochrane,G., Duggan,K., Eberhardt,R. et al. (2004) The EMBL Nucleotide Sequence Database. Nucleic Acids Res., 32, D27–D30. - PMC - PubMed
    1. 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. - PMC - PubMed
    1. Berman H., Henrick,K. and Nakamura,H. (2003) Announcing the worldwide Protein Data Bank. Nature Struct. Biol., 10, 980. - PubMed
    1. Coulson A.F. and Moult,J. (2002) A unifold, mesofold, and superfold model of protein fold use. Proteins, 46, 61–71. - PubMed
    1. Wheeler D.L., Church,D.M., Edgar,R., Federhen,S., Helmberg,W., Madden,T.L., Pontius,J.U., Schuler,G.D., Schriml,L.M., Sequeira,E. et al. (2004) Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res., 32, D35–D40. - PMC - PubMed

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