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Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction
BACKGROUND: Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural information embedded in fragment libraries has not been systematically extracted...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240311/ https://www.ncbi.nlm.nih.gov/pubmed/34182922 http://dx.doi.org/10.1186/s12859-021-04258-6 |
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author | Liu, Siyuan Wang, Tong Xu, Qijiang Shao, Bin Yin, Jian Liu, Tie-Yan |
author_facet | Liu, Siyuan Wang, Tong Xu, Qijiang Shao, Bin Yin, Jian Liu, Tie-Yan |
author_sort | Liu, Siyuan |
collection | PubMed |
description | BACKGROUND: Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural information embedded in fragment libraries has not been systematically extracted and used beyond fragment assembly. METHODS: To better leverage the valuable structural information for protein structure prediction, we extracted seven types of structural information from fragment libraries. We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. RESULTS: Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. CONCLUSION: Our work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04258-6. |
format | Online Article Text |
id | pubmed-8240311 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-82403112021-06-30 Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction Liu, Siyuan Wang, Tong Xu, Qijiang Shao, Bin Yin, Jian Liu, Tie-Yan BMC Bioinformatics Research BACKGROUND: Fragment libraries play a key role in fragment-assembly based protein structure prediction, where protein fragments are assembled to form a complete three-dimensional structure. Rich and accurate structural information embedded in fragment libraries has not been systematically extracted and used beyond fragment assembly. METHODS: To better leverage the valuable structural information for protein structure prediction, we extracted seven types of structural information from fragment libraries. We broadened the usage of such structural information by transforming fragment libraries into protein-specific potentials for gradient-descent based protein folding and encoding fragment libraries as structural features for protein property prediction. RESULTS: Fragment libraires improved the accuracy of protein folding and outperformed state-of-the-art algorithms with respect to predicted properties, such as torsion angles and inter-residue distances. CONCLUSION: Our work implies that the rich structural information extracted from fragment libraries can complement sequence-derived features to help protein structure prediction. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04258-6. BioMed Central 2021-06-28 /pmc/articles/PMC8240311/ /pubmed/34182922 http://dx.doi.org/10.1186/s12859-021-04258-6 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Liu, Siyuan Wang, Tong Xu, Qijiang Shao, Bin Yin, Jian Liu, Tie-Yan Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title | Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title_full | Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title_fullStr | Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title_full_unstemmed | Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title_short | Complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
title_sort | complementing sequence-derived features with structural information extracted from fragment libraries for protein structure prediction |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8240311/ https://www.ncbi.nlm.nih.gov/pubmed/34182922 http://dx.doi.org/10.1186/s12859-021-04258-6 |
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