Abstract
JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.
Highlights
Knowledge of a protein’s three-dimensional structure is central to understanding the protein’s detailed function
There is a need for accurate methods to predict structural and functional features from the amino acid sequence
In this paper we summarize the current performance and features of the upgraded JPred server (JPred4) which incorporates the secondary structure and solvent accessibility prediction program JNet v.2.3.1
Summary
Knowledge of a protein’s three-dimensional structure is central to understanding the protein’s detailed function. There is a need for accurate methods to predict structural and functional features from the amino acid sequence. Hundreds of papers have been published describing methods for protein secondary structure prediction, three of the most widely used are JPred, PSIPRED and PredictProtein.
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