Jpred v.4 is the latest version of the JPred
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
Secondary Structure Prediction Server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction,
that has existed since 1998 in different versions.
In addition to
protein secondary structure
Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure ...
, JPred also makes predictions of solvent accessibility and
coiled-coil
A coiled coil is a structural motif in proteins in which 2–7
alpha helix, alpha-helices are coiled together like the strands of a rope. (Protein dimer, Dimers and Protein trimer, trimers are the most common types.) Many coiled coil-type protei ...
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.
JPred 2
The static HTML pages of JPred 2 are still available for reference.
JPred 3
The JPred v3 followed on from previous versions of JPred developed and maintained by James Cuff and Jonathan Barber (see JPred References). 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
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences. A BLA ...
hits to the query
* PS/PDF output now incorporates all the predictions
JPred 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%.
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* 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.
* Added prediction jobs monitoring tools.
* 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.
Sequence residues are categorised or assigned to one of the secondary structure elements, such as ]alpha-helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...
, beta-sheet
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a g ...
and coiled-coil.
Jnet uses two neural network
A neural network is a network or circuit of biological neurons, or, in a modern sense, an artificial neural network, composed of artificial neurons or nodes. Thus, a neural network is either a biological neural network, made up of biological ...
s for its prediction. The first network is fed with a window of 17 residues over each amino acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha am ...
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.
See also
* PSIPRED
* List of protein structure prediction software
This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ''ab initio'' methods, secondary structure prediction, and transmembrane ...
References
{{Reflist
Structural bioinformatics software
Artificial neural networks