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SIFTS mapping files between PDB and UniProt, Pfam, EC, CATH, SCOP, GO, etc. available from PDBe

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  • Gerard DVD Kleywegt
    The Protein Data Bank in Europe (PDBe; http://pdbe.org/) is pleased to announce the Structure Integration with Function, Taxonomy and Sequence (SIFTS)
    Message 1 of 1 , Sep 17, 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@... ..................... pdbe.org
      Secretary: Pauline Haslam pdbe_admin@...
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