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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]
This article provides insufficient context for those unfamiliar with the subject. (May 2018) |
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]
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:
The current version of JPred (v4) has the following improvements and updates incorporated:
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]
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