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Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures
Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9155634/ https://www.ncbi.nlm.nih.gov/pubmed/35189634 http://dx.doi.org/10.1093/bib/bbac025 |
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author | Pan, Qisheng Nguyen, Thanh Binh Ascher, David B Pires, Douglas E V |
author_facet | Pan, Qisheng Nguyen, Thanh Binh Ascher, David B Pires, Douglas E V |
author_sort | Pan, Qisheng |
collection | PubMed |
description | Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures. These, however, have been developed and validated using experimentally derived structures and biophysical measurements. A large proportion of protein structures remain to be experimentally elucidated and, while many studies have based their conclusions on predictions made using homology models, there has been no systematic evaluation of the reliability of these tools in the absence of experimental structural data. We have, therefore, systematically investigated the performance and robustness of ten widely used structural methods when presented with homology models built using templates at a range of sequence identity levels (from 15% to 95%) and contrasted performance with sequence-based tools, as a baseline. We found there is indeed performance deterioration on homology models built using templates with sequence identity below 40%, where sequence-based tools might become preferable. This was most marked for mutations in solvent exposed residues and stabilizing mutations. As structure prediction tools improve, the reliability of these predictors is expected to follow, however we strongly suggest that these factors should be taken into consideration when interpreting results from structure-based predictors of mutation effects on protein stability. |
format | Online Article Text |
id | pubmed-9155634 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-91556342022-06-04 Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures Pan, Qisheng Nguyen, Thanh Binh Ascher, David B Pires, Douglas E V Brief Bioinform Review Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods have been developed to try to estimate the effects of missense mutations on protein stability, leveraging growing availability of protein 3D structures. These, however, have been developed and validated using experimentally derived structures and biophysical measurements. A large proportion of protein structures remain to be experimentally elucidated and, while many studies have based their conclusions on predictions made using homology models, there has been no systematic evaluation of the reliability of these tools in the absence of experimental structural data. We have, therefore, systematically investigated the performance and robustness of ten widely used structural methods when presented with homology models built using templates at a range of sequence identity levels (from 15% to 95%) and contrasted performance with sequence-based tools, as a baseline. We found there is indeed performance deterioration on homology models built using templates with sequence identity below 40%, where sequence-based tools might become preferable. This was most marked for mutations in solvent exposed residues and stabilizing mutations. As structure prediction tools improve, the reliability of these predictors is expected to follow, however we strongly suggest that these factors should be taken into consideration when interpreting results from structure-based predictors of mutation effects on protein stability. Oxford University Press 2022-02-21 /pmc/articles/PMC9155634/ /pubmed/35189634 http://dx.doi.org/10.1093/bib/bbac025 Text en © The Author(s) 2022. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Review Pan, Qisheng Nguyen, Thanh Binh Ascher, David B Pires, Douglas E V Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title | Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title_full | Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title_fullStr | Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title_full_unstemmed | Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title_short | Systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
title_sort | systematic evaluation of computational tools to predict the effects of mutations on protein stability in the absence of experimental structures |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9155634/ https://www.ncbi.nlm.nih.gov/pubmed/35189634 http://dx.doi.org/10.1093/bib/bbac025 |
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