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. 2019 Jul 2;47(W1):W402-W407.
doi: 10.1093/nar/gkz297.

The PSIPRED Protein Analysis Workbench: 20 years on

Daniel W A Buchan  1 , David T Jones  1
Affiliations

The PSIPRED Protein Analysis Workbench: 20 years on

Daniel W A Buchan et al. Nucleic Acids Res. .

Abstract

The PSIPRED Workbench is a web server offering a range of predictive methods to the bioscience community for 20 years. Here, we present the work we have completed to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years. The main focus of our recent website upgrade work has been the acceleration of analyses in the face of increasing protein sequence database size. We additionally discuss any new software, the new hardware infrastructure, our webservices and web site. Lastly we survey updates to some of the key predictive algorithms available through our website.

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Figures

Figure 1.
Figure 1.
The new website layout. (A) Users select which kind of data they have to analyse, either protein Sequence data or a PDB file. (B) Users are presented with the set of 12 sequence analysis algorithms available on the site. Sequence analysis jobs present users with the sequence results page (D), the main panel shows the sequence annotation map and further results and tables are presented below. On the right hand side, a panel to download results files and to resubmit sequence segments is shown. For PDB analyses (C), users are presented with the four PDB structure analysis tools. PDB results (E), typically show the predictions annotated on the PDB file that was submitted, again results files can be downloaded from the panel on the right.
Figure 2.
Figure 2.
The new results presentation. Area A is the header section returning the submission name the user provided and the ability to copy the results page URL. Area B contains the file Download panel which are either available individually or as a zip file. Area C holds the Segment Resubmission panel which lets users select a sub-segment of the query sequence to re-submit to the server. Area D is the Sequence Annotation Plot. This shows the user's query sequence and any predictions annotated on it, in this instance it shows a PSIPRED secondary structure prediction. The sequence annotation panel is not displayed for structure prediction results. Areal E shows one or more further results panels, in this case it shows the PSIPRED results cartoon.
See this image and copyright information in PMC

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