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Quantifying side-chain conformational variations in protein structure
Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109468/ https://www.ncbi.nlm.nih.gov/pubmed/27845406 http://dx.doi.org/10.1038/srep37024 |
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author | Miao, Zhichao Cao, Yang |
author_facet | Miao, Zhichao Cao, Yang |
author_sort | Miao, Zhichao |
collection | PubMed |
description | Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. |
format | Online Article Text |
id | pubmed-5109468 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-51094682016-11-25 Quantifying side-chain conformational variations in protein structure Miao, Zhichao Cao, Yang Sci Rep Article Protein side-chain conformation is closely related to their biological functions. The side-chain prediction is a key step in protein design, protein docking and structure optimization. However, side-chain polymorphism comprehensively exists in protein as various types and has been long overlooked by side-chain prediction. But such conformational variations have not been quantitatively studied and the correlations between these variations and residue features are vague. Here, we performed statistical analyses on large scale data sets and found that the side-chain conformational flexibility is closely related to the exposure to solvent, degree of freedom and hydrophilicity. These analyses allowed us to quantify different types of side-chain variabilities in PDB. The results underscore that protein side-chain conformation prediction is not a single-answer problem, leading us to reconsider the assessment approaches of side-chain prediction programs. Nature Publishing Group 2016-11-15 /pmc/articles/PMC5109468/ /pubmed/27845406 http://dx.doi.org/10.1038/srep37024 Text en Copyright © 2016, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Miao, Zhichao Cao, Yang Quantifying side-chain conformational variations in protein structure |
title | Quantifying side-chain conformational variations in protein structure |
title_full | Quantifying side-chain conformational variations in protein structure |
title_fullStr | Quantifying side-chain conformational variations in protein structure |
title_full_unstemmed | Quantifying side-chain conformational variations in protein structure |
title_short | Quantifying side-chain conformational variations in protein structure |
title_sort | quantifying side-chain conformational variations in protein structure |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109468/ https://www.ncbi.nlm.nih.gov/pubmed/27845406 http://dx.doi.org/10.1038/srep37024 |
work_keys_str_mv | AT miaozhichao quantifyingsidechainconformationalvariationsinproteinstructure AT caoyang quantifyingsidechainconformationalvariationsinproteinstructure |