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:

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:

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

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
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