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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Main Authors:	Wang, Sheng, Li, Wei, Zhang, Renyu, Liu, Shiwang, Xu, Jinbo
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987891/

id	pubmed-4987891
recordtype	oai_dc
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 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
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Wang, Sheng Li, Wei Zhang, Renyu Liu, Shiwang Xu, Jinbo
spellingShingle	Wang, Sheng Li, Wei Zhang, Renyu Liu, Shiwang Xu, Jinbo CoinFold: a web server for protein contact prediction and contact-assisted protein folding
author_facet	Wang, Sheng Li, Wei Zhang, Renyu Liu, Shiwang Xu, Jinbo
author_sort	Wang, Sheng
title	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_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_sort	coinfold: a web server for protein contact prediction and contact-assisted protein folding
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.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987891/
_version_	1613628880503963648

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

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