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 3edit
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
JPred 4edit
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.[8]
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.[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]
^"JPred4 monitoring tools". Retrieved 16 July 2015.
^"JPred4 Help and Tutorials". Retrieved 16 July 2015.
^Cuff, JA; Barton, GJ (August 2000). "Application of multiple sequence alignment profiles to improve protein secondary structure prediction". Proteins. 40 (3): 502–11. doi:10.1002/1097-0134(20000815)40:3<502::aid-prot170>3.0.co;2-q. PMID 10861942. S2CID 855816.
December 18, 2023
jpred, this, article, provides, insufficient, context, those, unfamiliar, with, subject, please, help, improve, article, providing, more, context, reader, 2018, learn, when, remove, this, template, message, latest, version, jpred, protein, secondary, structure. This article provides insufficient context for those unfamiliar with the subject Please help improve the article by providing more context for the reader May 2018 Learn how and when to remove this template message 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 Contents 1 JPred 2 2 JPred 3 3 JPred 4 4 See also 5 ReferencesJPred 2 editThe static HTML pages of JPred 2 are still available for reference 5 JPred 3 editThe 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 gt 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 predictionsJPred 4 editThe 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 gt 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 8 Added prediction jobs monitoring tools 9 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 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 editPSIPRED List of protein structure prediction softwareReferences edit JPred4 A Protein Secondary Structure Prediction Server Retrieved 16 July 2015 a b Drozdetskiy Alexey Cole Chris Procter James Barton Geoffrey Apr 16 2015 JPred4 a protein secondary structure prediction server Nucleic Acids Research 43 W1 W389 W394 doi 10 1093 nar gkv332 PMC 4489285 PMID 25883141 JPred old news Oct 25 1998 Retrieved 16 Jul 2015 JPred4 statistics Retrieved 16 July 2015 JPred2 legacy Retrieved 16 July 2015 JPred3 previous version of JPred Retrieved 16 July 2015 JPred4 references Retrieved 16 July 2015 JPred4 RESTful API Retrieved 16 July 2015 JPred4 monitoring tools Retrieved 16 July 2015 JPred4 Help and Tutorials Retrieved 16 July 2015 Cuff JA Barton GJ August 2000 Application of multiple sequence alignment profiles to improve protein secondary structure prediction Proteins 40 3 502 11 doi 10 1002 1097 0134 20000815 40 3 lt 502 aid prot170 gt 3 0 co 2 q PMID 10861942 S2CID 855816 Retrieved from https en wikipedia org w index php title Jpred amp oldid 1130827306, wikipedia, wiki, book, books, library,
