Jpred
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Jpred v.4 is the latest version of the 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 static HTML pages of JPred 2 are still available for reference.[5]
JPred 3
The JPred v3[6] followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References[7]). This release added new functionality and fixed many 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