InterProScan 5: Large scale protein function classification

Abstract: InterPro (http://www.ebi.ac.uk/interpro/) is a freely available resource that is used to classify sequences into protein families and to predict the presence of important domains and sites. InterProScan (https://www.ebi.ac.uk/interpro/interproscan.html) is the underlying software application that allows both protein and nucleic acid sequences to be scanned against InterPro's predictive models (signatures), which are provided by the resource’s member databases. Recently, both the Conserved Domain Database (CDD) and Structure-Function Linkage Database (SFLD) have joined InterPro as new member databases. InterProScan has been updated accordingly, incorporating CDD’s curated models that use position specific scoring matrices (PSSMs) to represent protein domains, which tend to be more functionally specific than some of the models already used in InterPro. SFLD’s hidden Markov models that offer structure-function mapping have also been incorporated. SFLD models allow evolutionary classification of related enzymes according to shared chemical functions to determine conserved active sites. Here, we present these recent developments and performance improvements to InterProScan. Optimisation in the pipeline filters  and database query refinements have also resulted in improved throughput for large-scale protein sequence analysis  and accelerated InterProScan domain searches by several orders of magnitude.