Scalable web services for the PSIPRED Protein Analysis Workbench - PubMed (original) (raw)

. 2013 Jul;41(Web Server issue):W349-57.

doi: 10.1093/nar/gkt381. Epub 2013 Jun 8.

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Scalable web services for the PSIPRED Protein Analysis Workbench

Daniel W A Buchan et al. Nucleic Acids Res. 2013 Jul.

Abstract

Here, we present the new UCL Bioinformatics Group's PSIPRED Protein Analysis Workbench. The Workbench unites all of our previously available analysis methods into a single web-based framework. The new web portal provides a greatly streamlined user interface with a number of new features to allow users to better explore their results. We offer a number of additional services to enable computationally scalable execution of our prediction methods; these include SOAP and XML-RPC web server access and new HADOOP packages. All software and services are available via the UCL Bioinformatics Group website at http://bioinf.cs.ucl.ac.uk/.

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Figures

Figure 1.

Figure 1.

Flowchart of the BioSerf2 automated homology modelling protocol. Incoming query sequences are independently matched to PDB chains using PSIBLAST, pGenTHREADER and HH. The three sets of models produced are then compared by the TMJury process, which produces up to 10 candidate homologous structures. These structures and their alignments to the query sequence are used as input for MODELLER to produce a single final structure.

Figure 2.

Figure 2.

The new front page of the PSIPRED Protein Analysis Workbench. The ‘Choose Prediction Method’ allows users to select any set of available analysis methods. A series of tabs appear along the top bar when users select analysis methods. These additional tabs allow users to select more detailed options.

Figure 3.

Figure 3.

A typical results page where a user has selected all the available analysis methods. The image shows the analysis summary front page of the results. (a) Tab bar: this region contains a range of tabs the users can select to explore the detailed results from each analysis method. (b) Secondary structure map: this area of the page lays out the query sequence and colours residues as per the annotations made by each analysis methods. If users have selected a MEMSAT-SVM prediction, they can use the buttons provided to toggle between the different sets of sequence annotations. Here, α-helical residues are in pink, β-strand residues are in yellow and putative domain boundaries are indicated in blue. (c) Sequence resubmission widget: this region contains a cartoon selector that represents the query sequence. Users can use the sliders to select any sub-sequence of their query sequence and then select further analyses to perform on just the selected sub-sequence. (d) GenTHREADER summary: if a GenTHREADER analysis was calculated, the final region presents several schematic cartoons of each GenTHREADER alignment. Hits are presented as bars coloured as per the GenTHEADER confidence scores, green for greatest confidence, orange of moderate confidence and red for lowest confidence. If the user ‘mouses over’ the bars, a pop-up presents more detailed information about the alignment region.

Figure 4.

Figure 4.

The results summary for UniProt sequence A9DA50. (a) The secondary structure map showing the PSIPRED secondary structure predictions. α-Helical residues are in pink, β-strand residues are in yellow and putative domain boundaries are indicated in blue. (b) The pGenTHREADER alignments summary. Alignments in green have high-statistical confidence.

Figure 5.

Figure 5.

The detailed pGenTHREADER results table for UniProt sequence A9DA50. The matched structures can all be seen to be similar all β-sheet structures. These are listed in CATH and PDBSum as either leucine-rich repeat domains or Tol-like receptors. Those chains fully classified in CATH list this domain in the 3.80.10-fold family.

Figure 6.

Figure 6.

The MEMSAT-SVM results for the N-terminal region of UniProt sequence A9DA50. MEMSAT-SVM predicts a single membrane spanning helix (in purple) in this region.

Figure 7.

Figure 7.

The results summary for the C-terminal region of UniProt sequence A9DA50. The secondary structure and pDomTHREADER results indicate that this region likely has a leading IG-like β-sheet domain.

Figure 8.

Figure 8.

The FFPRED output for UniProt sequence A9DA50 indicating the best matched GO terms. Only the first 10 terms from the list are shown.

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