Dear colleagues,
Data on sequence level mapping through the SIFTS process
<https://www.ebi.ac.uk/pdbe/docs/sifts/> can now be retrieved directly
from updated mmCIF files, available on PDBe entry pages. These files now
contain residue-level mapping between UniProt and PDB entries, including
coordinate numbering for UniProt accessions and mapping to a host of
other protein resources.
PDBe’s release process creates ‘updated’ PDBx/mmCIF files from PDB
archive files, containing remapped enumerations and additional
information, while yielding more consistent, standardised metadata,
without altering core PDB information, such as atomic coordinates and
experimental data. These updated PDBx/mmCIF files have now been further
enriched by the addition of three new ‘SIFTS- specific’ categories,
providing improved mapping between structure and sequence data.
SIFTS provides residue-level mapping between UniProt and PDB entries,
while also incorporating annotation from the IntEnz, GO, InterPro, Pfam,
CATH, SCOP, SCOP2, PubMed, Ensembl and Homologene resources. The
information is updated and released every Wednesday concurrently with
the release of new PDB entries and can be obtained from the PDBe Rest
API <https://www.ebi.ac.uk/pdbe/api/doc/sifts.html> or PDB entry XML
files in the EMBL-EBI FTP <ftp://ftp.ebi.ac.uk/pub/databases/msd/sifts/>
area. Following this update to the updated PDBx/mmCIF files produced by
PDBe, SIFTS data can also be directly retrieved from these files and are
available from PDBe entry pages.
For more information, visit
https://www.ebi.ac.uk/pdbe/about/news/sifts-data-now-included-pdbe-mmcif-files
Kind Regards,
David Armstrong
--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544
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