JPred4

a protein secondary structure prediction server

Alexey Drozdetskiy, Christian Cole, James Procter, Geoffrey J. Barton (Lead / Corresponding author)

Research output: Contribution to journalArticle

506 Citations (Scopus)
218 Downloads (Pure)

Abstract

JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.

Original languageEnglish
Pages (from-to)W389-W394
Number of pages6
JournalNucleic Acids Research
Volume43
Issue numberW1
Early online date16 Apr 2015
DOIs
Publication statusPublished - 1 Jul 2015

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Secondary Protein Structure
Sequence Alignment
Equipment and Supplies

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title = "JPred4: a protein secondary structure prediction server",
abstract = "JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0{\%} while solvent accessibility prediction accuracy has been raised to 90{\%} for residues <5{\%} accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.",
author = "Alexey Drozdetskiy and Christian Cole and James Procter and Barton, {Geoffrey J.}",
note = "{\circledC} The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.",
year = "2015",
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JPred4 : a protein secondary structure prediction server. / Drozdetskiy, Alexey; Cole, Christian; Procter, James; Barton, Geoffrey J. (Lead / Corresponding author).

In: Nucleic Acids Research, Vol. 43, No. W1, 01.07.2015, p. W389-W394.

Research output: Contribution to journalArticle

TY - JOUR

T1 - JPred4

T2 - a protein secondary structure prediction server

AU - Drozdetskiy, Alexey

AU - Cole, Christian

AU - Procter, James

AU - Barton, Geoffrey J.

N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

PY - 2015/7/1

Y1 - 2015/7/1

N2 - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.

AB - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. The JPred service runs up to 94 000 jobs per month and has carried out over 1.5 million predictions in total for users in 179 countries. The JPred4 web server has been re-implemented in the Bootstrap framework and JavaScript to improve its design, usability and accessibility from mobile devices. JPred4 features higher accuracy, with a blind three-state (α-helix, β-strand and coil) secondary structure prediction accuracy of 82.0% while solvent accessibility prediction accuracy has been raised to 90% for residues <5% accessible. Reporting of results is enhanced both on the website and through the optional email summaries and batch submission results. Predictions are now presented in SVG format with options to view full multiple sequence alignments with and without gaps and insertions. Finally, the help-pages have been updated and tool-tips added as well as step-by-step tutorials.

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DO - 10.1093/nar/gkv332

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VL - 43

SP - W389-W394

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JF - Nucleic Acids Research

SN - 0305-1048

IS - W1

ER -