[X-plor] SIFTS mapping files between PDB and UniProt, Pfam, EC, CATH, SCOP, GO, etc. available from PDBe

Gerard DVD Kleywegt via x-plor%40net.bio.net (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); 
doi:10.1093/nar/gki058).

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

                           pdbe.org/sifts

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 
pages).

--Gerard

---
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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