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CoinFold: a web server for protein contact prediction and contact-assisted protein folding

CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analys...

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Detalles Bibliográficos
Autores principales: Wang, Sheng, Li, Wei, Zhang, Renyu, Liu, Shiwang, Xu, Jinbo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987891/
https://www.ncbi.nlm.nih.gov/pubmed/27112569
http://dx.doi.org/10.1093/nar/gkw307
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author Wang, Sheng
Li, Wei
Zhang, Renyu
Liu, Shiwang
Xu, Jinbo
author_facet Wang, Sheng
Li, Wei
Zhang, Renyu
Liu, Shiwang
Xu, Jinbo
author_sort Wang, Sheng
collection PubMed
description CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction.
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spelling pubmed-49878912016-08-22 CoinFold: a web server for protein contact prediction and contact-assisted protein folding Wang, Sheng Li, Wei Zhang, Renyu Liu, Shiwang Xu, Jinbo Nucleic Acids Res Web Server issue CoinFold (http://raptorx2.uchicago.edu/ContactMap/) is a web server for protein contact prediction and contact-assisted de novo structure prediction. CoinFold predicts contacts by integrating joint multi-family evolutionary coupling (EC) analysis and supervised machine learning. This joint EC analysis is unique in that it not only uses residue coevolution information in the target protein family, but also that in the related families which may have divergent sequences but similar folds. The supervised learning further improves contact prediction accuracy by making use of sequence profile, contact (distance) potential and other information. Finally, this server predicts tertiary structure of a sequence by feeding its predicted contacts and secondary structure to the CNS suite. Tested on the CASP and CAMEO targets, this server shows significant advantages over existing ones of similar category in both contact and tertiary structure prediction. Oxford University Press 2016-07-08 2016-04-25 /pmc/articles/PMC4987891/ /pubmed/27112569 http://dx.doi.org/10.1093/nar/gkw307 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server issue
Wang, Sheng
Li, Wei
Zhang, Renyu
Liu, Shiwang
Xu, Jinbo
CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title_full CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title_fullStr CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title_full_unstemmed CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title_short CoinFold: a web server for protein contact prediction and contact-assisted protein folding
title_sort coinfold: a web server for protein contact prediction and contact-assisted protein folding
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987891/
https://www.ncbi.nlm.nih.gov/pubmed/27112569
http://dx.doi.org/10.1093/nar/gkw307
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