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. 2019 Jan 8;47(D1):D482-D489.
doi: 10.1093/nar/gky1114.

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

Jose M Dana  1 , Aleksandras Gutmanas  1 , Nidhi Tyagi  2 , Guoying Qi  2 , Claire O'Donovan  3 , Maria Martin  2 , Sameer Velankar  1
Affiliations

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

Jose M Dana et al. Nucleic Acids Res. .

Abstract

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts/) was established in 2002 and continues to operate as a collaboration between the Protein Data Bank in Europe (PDBe; http://pdbe.org) and the UniProt Knowledgebase (UniProtKB; http://uniprot.org). The resource is instrumental in the transfer of annotations between protein structure and protein sequence resources through provision of up-to-date residue-level mappings between entries from the PDB and from UniProtKB. SIFTS also incorporates residue-level annotations from other biological resources, currently comprising the NCBI taxonomy database, IntEnz, GO, Pfam, InterPro, SCOP, CATH, PubMed, Ensembl, Homologene and automatic Pfam domain assignments based on HMM profiles. The recently released implementation of SIFTS includes support for multiple cross-references for proteins in the PDB, allowing mappings to UniProtKB isoforms and UniRef90 cluster members. This development makes structure data in the PDB readily available to over 1.8 million UniProtKB accessions.

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Figures

Figure 1.
Figure 1.
Schematic diagrams of the SIFTS process. (A) Overall view of the data flow from PDB, UniProtKB and other resources to data distribution. (B) Calculation of direct mappings between protein structures in PDB and UniProtKB sequences, including isoforms. The process in panel B is invoked weekly and the data are released concurrently with the release of new PDB structures (see text). (C) Calculation of mappings for UniRef90 dataset. The process in panel C is invoked after the weekly release of new PDB structures.
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