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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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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. |
format | Online Article Text |
id | pubmed-4987891 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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