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A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
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SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in
Jose M Dana1, Aleksandras Gutmanas1, Nidhi Tyagi2
1Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Nucleic Acids Research
|November 17, 2018
Summary
The Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource links protein structure data with sequence information. This enables broader access to protein data by mapping PDB entries to UniProtKB, enhancing biological research.
Area of Science:
- Structural Biology
- Bioinformatics
- Protein Science
Background:
- The Structure Integration with Function, Taxonomy and Sequences (SIFTS) resource facilitates annotation transfer between protein structure and sequence databases.
- It is a collaborative effort between the Protein Data Bank in Europe (PDBe) and the UniProt Knowledgebase (UniProtKB).
Purpose of the Study:
- To provide up-to-date residue-level mappings between Protein Data Bank (PDB) and UniProtKB entries.
- To integrate diverse biological annotations at the residue level from various resources.
- To enhance accessibility of PDB structure data to a larger user base.
Main Methods:
- Development and maintenance of residue-level mappings between PDB and UniProtKB.
- Integration of annotations from external biological databases (e.g., NCBI taxonomy, GO, Pfam, SCOP, CATH).
- Implementation of support for multiple cross-references, including UniProtKB isoforms and UniRef90 clusters.
Main Results:
- SIFTS provides comprehensive residue-level mappings, enabling seamless annotation transfer.
- The resource incorporates a wide array of biological annotations, enriching protein data.
- Recent updates allow PDB structure data to be linked to over 1.8 million UniProtKB accessions.
Conclusions:
- SIFTS is a crucial resource for integrating and accessing protein structure-function-taxonomy-sequence information.
- The enhanced cross-referencing capabilities significantly increase the discoverability and utility of PDB data.
- This facilitates more comprehensive analysis in structural biology and related fields.
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