[Protein-crystallography] SIFTS mapping files between PDB and
UniProt, Pfam, EC, CATH, SCOP, GO, etc. available from PDBe
Gerard DVD Kleywegt
(by gerard from xray.bmc.uu.se)
Fri Sep 17 10:49:59 EST 2010
The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to
announce the "Structure Integration with Function, Taxonomy and Sequence"
(SIFTS) initiative, a close collaboration between PDBe and UniProt, that aims
to improve the integration of the structural database and other bioinformatics
resources (see Velankar et al., Nucleic Acids Research 33, D262-265 (2005);
SIFTS is the authoritative source of up-to-date residue-level annotation of
protein structures in the PDB with data available in UniProt, NCBI taxonomy,
IntEnz, CATH, SCOP, GO, InterPro, Pfam and Pubmed. As of 16 September 2010
up-to-date mapping information for 64073 PDB entries is provided. SIFTS itself
is used by major resources such as PDBe, RCSB, PDBsum, Pfam, SCOP, InterPro,
DAS-server providers (http://www.dasregistry.org/) and many other
bioinformatics research and service groups around the world.
The data included in SIFTS is available through the website
This includes a compressed XML file for every individual mapped entry (with
details of mappings at the level of residues) as well as overview files that
provide tab-delimited lists of, e.g., the correspondence between all PDB
entries and CATH, EC, UniProt, etc. For details, click on the "Quick Access"
button on the SIFTS website.
If you ever want to study such mappings, please note that the corresponding
annotation in PDB and mmCIF files available in the PDB is not necessarily
up-to-date (it was correct at the time of processing, but is not updated after
that). In such cases, please retrieve your data from the authoritative source
of mapping information - SIFTS.
As always, PDBe welcomes comments and suggestions about its resources and
services (preferably using the big, fat "FEEDBACK" button on the PDBe web
Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK
gerard from ebi.ac.uk ..................... pdbe.org
Secretary: Pauline Haslam pdbe_admin from ebi.ac.uk
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