Mapping PDB chains to UniProtKB entries.
BACKGROUND
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.


BACKGROUND
The resource may be queried interactively or downloaded from http://www.bioinf.org.uk/pdbsws/.
Martin
Andrew C R
AC
Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK. andrew@bioinf.org.uk
D000595:Amino Acid Sequence; D001331:Automation; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D016208:Databases, Factual; D030562:Databases, Protein; D001330:Electronic Data Processing; D016247:Information Storage and Retrieval; D020407:Internet; D008377:Maps as Topic; D008869:Microtubule-Associated Proteins / Q000737:chemistry; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software
D008869:Microtubule-Associated Proteins; D011506:Proteins