JPred4: a protein secondary structure prediction server

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.

Figure 1.

(1) Screenshot of the JPred4 job submission page with single sequence submission field (2) and an example of a tool-tip message (3). Advanced options are opened on request (4) and include input file upload, format selection (5) as well as optional email and query name fields (6). (7) Job progress page with access to the detailed job run log file (8).

Figure 2.

JPred4 results summary page (1) with the results of predictions presented in SVG (2). Links to detailed and simple reports in coloured HTML/PS/PDF formats (3). Example summary in HTML format is shown in (4) as well as the new addition of full multiple sequence alignments with and without gaps/insertions (5). On a separate linked page the user is able to run the Jalview applet (6) which allows a more sophisticated and interactive method of viewing the prediction results. Links to all the details for the prediction and an archive of the results are also available (7).

Figure 3.

(1) Illustration of a single sequence job submission secondary structure prediction results summary email with link to full result details (2). (3) Illustration of a batch submission email summary with overall and per job (4) details that give links to individual predictions and an archive with all results for all sequences submitted in the batch.