SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
08 01 2019
08 01 2019
Historique:
received:
07
09
2018
accepted:
22
10
2018
pubmed:
18
11
2018
medline:
26
5
2020
entrez:
17
11
2018
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 30445541
pii: 5184711
doi: 10.1093/nar/gky1114
pmc: PMC6324003
doi:
Substances chimiques
Enzymes
0
Protein Isoforms
0
Proteins
0
Proteome
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
D482-D489Subventions
Organisme : Wellcome Trust
ID : 104948
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U41 HG007822
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/M011674/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 104948
Pays : United Kingdom
Références
Nat Struct Biol. 2003 Dec;10(12):980
pubmed: 14634627
Am J Hum Genet. 2018 Jan 4;102(1):11-26
pubmed: 29304370
Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199
pubmed: 27899635
Nucleic Acids Res. 2017 Jan 4;45(D1):D282-D288
pubmed: 27789697
Nucleic Acids Res. 2012 Jan;40(Database issue):D136-43
pubmed: 22139910
Nucleic Acids Res. 2018 Jan 4;46(D1):D21-D29
pubmed: 29186510
Nucleic Acids Res. 2017 Jan 4;45(D1):D158-D169
pubmed: 27899622
Nucleic Acids Res. 2018 Jul 2;46(W1):W200-W204
pubmed: 29905871
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D434-7
pubmed: 14681451
Nucleic Acids Res. 2018 Jan 4;46(D1):D754-D761
pubmed: 29155950
Nucleic Acids Res. 2017 Jan 4;45(D1):D271-D281
pubmed: 27794042
Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655
pubmed: 29145629
Protein Sci. 2018 Jan;27(1):129-134
pubmed: 28875543
Nucleic Acids Res. 2018 Jan 4;46(D1):D471-D476
pubmed: 29136219
Nucleic Acids Res. 2018 Jan 4;46(D1):D8-D13
pubmed: 29140470
Nucleic Acids Res. 2018 Jan 4;46(D1):D486-D492
pubmed: 29126160
Bioinformatics. 2006 Jul 1;22(13):1658-9
pubmed: 16731699
Bioinformatics. 2015 Mar 15;31(6):926-32
pubmed: 25398609
Nucleic Acids Res. 2019 Jan 8;47(D1):D520-D528
pubmed: 30357364
Proteins. 2013 Apr;81(4):583-91
pubmed: 23180575
Curr Protoc Bioinformatics. 2017 Dec 8;60:3.15.1-3.15.23
pubmed: 29220076
F1000Res. 2016 Sep 30;5:
pubmed: 27803796
Curr Protoc Bioinformatics. 2015 Mar 09;49:1.26.1-1.26.21
pubmed: 25754991
Elife. 2017 Oct 30;6:
pubmed: 29083299
Nucleic Acids Res. 2013 Jan;41(Database issue):D483-9
pubmed: 23203869
Nucleic Acids Res. 2016 Jan 4;44(D1):D385-95
pubmed: 26476444
Nucleic Acids Res. 2017 Jan 4;45(D1):D289-D295
pubmed: 27899584
Nucleic Acids Res. 2018 Jan 4;46(D1):D435-D439
pubmed: 29112716
Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85
pubmed: 26673716
Nucleic Acids Res. 2015 Jan;43(Database issue):D1057-63
pubmed: 25378336
Nucleic Acids Res. 2008 Jan;36(Database issue):D419-25
pubmed: 18000004