PredictProtein—an open resource for online prediction of protein structural and functional features

TLDR

PredictProtein is a long‑standing meta‑service for protein sequence analysis, providing structural and functional predictions since 1992 and freely available online. The aim is to create a user‑friendly system that serves experimentalists lacking advanced bioinformatics expertise. By submitting a protein sequence, users obtain multiple sequence alignments and predictions of secondary structure, solvent accessibility, transmembrane helices, strands, coiled‑coil regions, disulfide bonds, disordered regions, functional sites (ConSurf), Gene Ontology terms (metastudent), subcellular localization (LocTree3), protein‑protein and protein‑polynucleotide binding sites (ISIS2, SomeNA), and mutation effects (SNAP2), all displayed as text and interactive figures.

Abstract

PredictProtein is a meta-service for sequence analysis that has been predicting structural and functional features of proteins since 1992. Queried with a protein sequence it returns: multiple sequence alignments, predicted aspects of structure (secondary structure, solvent accessibility, transmembrane helices (TMSEG) and strands, coiled-coil regions, disulfide bonds and disordered regions) and function. The service incorporates analysis methods for the identification of functional regions (ConSurf), homology-based inference of Gene Ontology terms (metastudent), comprehensive subcellular localization prediction (LocTree3), protein–protein binding sites (ISIS2), protein–polynucleotide binding sites (SomeNA) and predictions of the effect of point mutations (non-synonymous SNPs) on protein function (SNAP2). Our goal has always been to develop a system optimized to meet the demands of experimentalists not highly experienced in bioinformatics. To this end, the PredictProtein results are presented as both text and a series of intuitive, interactive and visually appealing figures. The web server and sources are available at http://ppopen.rostlab.org.