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Protocols

SIFTS specifications

Information


Unique identifier OMICS_17454
Name SIFTS
Alternative name Structure integration with function taxonomy and sequence
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Output format XML
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Sameer Velankar

Publications for Structure integration with function taxonomy and sequence

SIFTS citations

 (34)
call_split

Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases

2018
PLoS Comput Biol
PMCID: 5919687
PMID: 29659563
DOI: 10.1371/journal.pcbi.1006101
call_split See protocol

[…] For each chain, a mapping to UniProt [] was performed using the SIFTS project []. Where available, mutation and natural variants data was retrieved for all binding site residues from the UniProt [] database. In total, 32 mutagenesis sites and 8 natural variants we […]

library_books

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates

2018
PMCID: 5890617
PMID: 29551288
DOI: 10.1016/j.str.2018.02.009

[…] A limitation of the methodology described is the potentially imprecise matching of PDB to KEGG via the EC reference number(s) in SIFTS. In many cases a PDB is uniquely matched to one KEGG reaction via its sole EC reference (38.8% of our dataset are uniquely mapped to one KEGG reaction in this way), but in some cases multiple EC […]

library_books

Prediction and interpretation of deleterious coding variants in terms of protein structural stability

2018
Sci Rep
PMCID: 5852127
PMID: 29540703
DOI: 10.1038/s41598-018-22531-2

[…] idue number, without any reference to a possible 3D structure. We had thus, in a second stage, to identify the subset of variants introduced in proteins that have an experimental structure, using the SIFTS webserver. We only considered the subset of mutations introduced in:globular proteins, or cytoplasmic or extracellular domains of membrane proteins;proteins with an X-ray structure available in […]

library_books

Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

2017
Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] ing between genomic and protein coordinate systems is error prone due to, for example, different genome assembly versions and alternative splicing. Where a mapping from genome to UniProt is possible, SIFTS [] and CRAVAT [] provide consistent residue-level mapping to and from PDB structures and other resources.Current tools that predict the effect of missense mutations are based on either protein s […]

library_books

Features of reactive cysteines discovered through computation: from kinase inhibition to enrichment around protein degrons

2017
Sci Rep
PMCID: 5703995
PMID: 29180682
DOI: 10.1038/s41598-017-15997-z

[…] and sites of sequence modification from the multiple species sets of the three cysteine modifications were associated with protein structures, where possible, using in-house code developed to use the SIFTS resource for mapping UniProt sequence numbers to PDB residue numbers. Structural coverage of specific regions in proteins (excluding the use of comparative models) is still rather limited, and t […]

library_books

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

2017
Nucleic Acids Res
PMCID: 5753225
PMID: 29126160
DOI: 10.1093/nar/gkx1070

[…] ogical systems. Cross-linking PDB data with other data resources also facilitates discovery of structure data. Since 2002, in collaboration with the UniProt team (), PDBe has developed and maintained SIFTS (Structure Integration with Function, Taxonomy and Sequence, ()), a resource providing residue-level mapping between UniProt KnowledgeBase (UniProtKB) and PDB entries, as well as annotations fro […]

Citations

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SIFTS institution(s)
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Protein Function Development, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Metabolomics, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
SIFTS funding source(s)
Supported by the UK Research and Innovation Biotechnology and Biological Sciences Research Council (BBSRC) [BB/M011674/1]; Wellcome Trust [104948]; European Union [284209]; National Institutes of Health [U41HG007822 and U24HG007822]; European Molecular Biology Laboratory (EMBL).

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