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Bioinformatics Advance Access originally published online on September 27, 2005
Bioinformatics 2005 21(23):4297-4301; doi:10.1093/bioinformatics/bti694
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Mapping PDB chains to UniProtKB entries

Andrew C. R. Martin

Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK

Motivation: UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.

Results: We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.

Availability: The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/

Contact: andrew{at}bioinf.org.uk

Received on July 29, 2005; revised on September 22, 2005; accepted on September 24, 2005

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