Jpred

Jpred v.4 is the latest version of the popular JPred Protein Secondary Structure Prediction Server^[1] which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction,^[2] that has existed since 1998 in different versions.^[3]

In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 134 000 jobs per month and has carried out over 2 million predictions in total for users in 179 countries.^[4]

The current version of JPred (v4) has the following improvements and updates incorporated:

• Retrained on the latest UniRef90 and SCOPe/ASTRAL version of Jnet (v2.3.1) - mean secondary structure prediction accuracy of >82%.^[2]
• Upgraded the Web Server to the latest technologies (Bootstrap framework, JavaScript) and updating the web pages – improving the design and usability through implementing responsive technologies.
• Added RESTful API and mass-submission and results retrieval scripts - resulting in peak throughput above 20,000 predictions per day.^[5]
• Added prediction jobs monitoring tools.^[6]
• Upgraded the results reporting – both, on the web-site, and through the optional email summary reports: improved batch submission, added results summary preview through Jalview results visualization summary in SVG and adding full multiple sequence alignments into the reports.
• Improved help-pages, incorporating tool-tips, and adding one-page step-by-step tutorials.^[7]

The JPred v3^[8] followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References^[9]). This release added new functionality and fixed lots of bugs. The highlights are:

• New, friendlier user interface
• Retrained and optimised version of Jnet (v2) - mean secondary structure prediction accuracy of >81%
• Batch submission of jobs
• Better error checking of input sequences/alignments
• Predictions now (optionally) returned via e-mail
• Users may provide their own query names for each submission
• JPred now makes a prediction even when there are no PSI-BLAST hits to the query
• PS/PDF output now incorporates all the predictions

The static HTML pages of JPred 2 are still available for reference.^[10]

Sequence residues are categorised or assigned to one of the secondary structure elements, such as alpha-helix, beta-sheet and coiled-coil.

Jnet uses two neural networks for its prediction. The first network is fed with a window of 17 residues over each amino acid in the alignment plus a conservation number. It uses a hidden layer of nine nodes and has three output nodes, one for each secondary structure element. The second network is fed with a window of 19 residues (the result of first network) plus the conservation number. It has a hidden layer with nine nodes and has three output nodes.^[11]

See also

• psipred
• Protein structure prediction software

References

1. ↑ "JPred4: A Protein Secondary Structure Prediction Server". Retrieved 16 July 2015. 
2. 1 2 Drozdetskiy, Alexey; Cole, Chris; Procter, James; Barton, Geoffrey (Apr 16, 2015). "JPred4: a protein secondary structure prediction server". Nucleic Acids Research. doi:10.1093/nar/gkv332. 
3. ↑ "JPred old news". Oct 25, 1998. Retrieved 16 Jul 2015. 
4. ↑ "JPred4 statistics". Retrieved 16 July 2015. 
5. ↑ "JPred4 RESTful API". Retrieved 16 July 2015. 
6. ↑ "JPred4 monitoring tools". Retrieved 16 July 2015. 
7. ↑ "JPred4 Help and Tutorials". Retrieved 16 July 2015. 
8. ↑ "JPred3: previous version of JPred". Retrieved 16 July 2015. 
9. ↑ "JPred4 references". Retrieved 16 July 2015. 
10. ↑ "JPred2: legacy". Retrieved 16 July 2015. 
11. ↑ Application of multiple sequence alignment profiles... [Proteins. 2000] - PubMed - NCBI