PIRSitePredict for protein functional site prediction using position-specific rules

Database : the Journal of Biological Databases and Curation
Chuming ChenCathy H Wu

Abstract

Methods focused on predicting 'global' annotations for proteins (such as molecular function, biological process and presence of domains or membership in a family) have reached a relatively mature stage. Methods to provide fine-grained 'local' annotation of functional sites (at the level of individual amino acid) are now coming to the forefront, especially in light of the rapid accumulation of genetic variant data. We have developed a computational method and workflow that predicts functional sites within proteins using position-specific conditional template annotation rules (namely PIR Site Rules or PIRSRs for short). Such rules are curated through review of known protein structural and other experimental data by structural biologists and are used to generate high-quality annotations for the UniProt Knowledgebase (UniProtKB) unreviewed section. To share the PIRSR functional site prediction method with the broader scientific community, we have streamlined our workflow and developed a stand-alone Java software package named PIRSitePredict. We demonstrate the use of PIRSitePredict for functional annotation of de novo assembled genome/transcriptome by annotating uncharacterized proteins from Trinity RNA-seq assembly of embryonic tr...Continue Reading

References

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Citations

May 14, 2020·Bioinformatics·Alistair MacDougallUNKNOWN UniProt Consortium

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Methods Mentioned

BETA
Glycosylation
RNA-seq

Software Mentioned

PIRSR
PIRSitePredict Annotation of Proteins ( HAMAP
Thymeleaf
Spring MVC
HMMER3
Phospho
Scan
UniRule
PIR
PIRSitePredict

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