SIFTS


30445541	SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. [PMID: 30445541] Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S. 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. Nucleic Acids Res. 2019:47(D1) \| 121 Citations (from Europe PMC, 2025-03-29)
23203869	SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. [PMID: 23203869] Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ. Abstract The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information. Nucleic Acids Res. 2013:41(Database issue) \| 159 Citations (from Europe PMC, 2025-03-29)

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. [PMID: 30445541]

Dana JM, Gutmanas A, Tyagi N, Qi G, O'Donovan C, Martin M, Velankar S.

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.

Nucleic Acids Res. 2019:47(D1) | 121 Citations (from Europe PMC, 2025-03-29)

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource. [PMID: 23203869]

Velankar S, Dana JM, Jacobsen J, van Ginkel G, Gane PJ, Luo J, Oldfield TJ, O'Donovan C, Martin MJ, Kleywegt GJ.

Abstract

The Structure Integration with Function, Taxonomy and Sequences resource (SIFTS; http://pdbe.org/sifts) is a close collaboration between the Protein Data Bank in Europe (PDBe) and UniProt. The two teams have developed a semi-automated process for maintaining up-to-date cross-reference information to UniProt entries, for all protein chains in the PDB entries present in the UniProt database. This process is carried out for every weekly PDB release and the information is stored in the SIFTS database. The SIFTS process includes cross-references to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy database. The information is exported in XML format, one file for each PDB entry, and is made available by FTP. Many bioinformatics resources use SIFTS data to obtain cross-references between the PDB and other biological databases so as to provide their users with up-to-date information.

Nucleic Acids Res. 2013:41(Database issue) | 159 Citations (from Europe PMC, 2025-03-29)

URL:	http://pdbe.org/sifts/
Full name:	Structure Integration with Function, Taxonomy and Sequence
Description:	SIFTS is an up-to-date resource for residue-level mapping between UniProt and PDB entries. The resource also provides residue-level annotation from the IntEnz,GO,Pfam,InterPro,SCOP,CATH and PubMed resources.
Year founded:	2013
Last update:	2013-01-01
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	DNA Protein
Data object:	NA
Database category:	Expression Interaction Standard ontology and nomenclature Structure
Major species:	NA
Keywords:	function protein residue-level mapping sequence taxonomy

University/Institution:	European Bioinformatics Institute
Address:	Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
City:	Cambridge
Province/State:	Cambridgeshire
Country/Region:	United Kingdom
Contact name (PI/Team):	Sameer Velankar
Contact email (PI/Helpdesk):	sameer@ebi.ac.uk

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Database Commons a catalog of worldwide biological databases