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Comparative analysis of web-based programs for single amino acid substitutions in proteins
Single amino-acid substitution in a protein affects its structure and function. These changes are the primary reasons for the advent of many complex diseases. Analyzing single point mutations in a protein is crucial to see their impact and to understand the disease mechanism. This has given many bio...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067658/ https://www.ncbi.nlm.nih.gov/pubmed/35507592 http://dx.doi.org/10.1371/journal.pone.0267084 |
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author | Choudhury, Arunabh Mohammad, Taj Anjum, Farah Shafie, Alaa Singh, Indrakant K. Abdullaev, Bekhzod Pasupuleti, Visweswara Rao Adnan, Mohd Yadav, Dharmendra Kumar Hassan, Md. Imtaiyaz |
author_facet | Choudhury, Arunabh Mohammad, Taj Anjum, Farah Shafie, Alaa Singh, Indrakant K. Abdullaev, Bekhzod Pasupuleti, Visweswara Rao Adnan, Mohd Yadav, Dharmendra Kumar Hassan, Md. Imtaiyaz |
author_sort | Choudhury, Arunabh |
collection | PubMed |
description | Single amino-acid substitution in a protein affects its structure and function. These changes are the primary reasons for the advent of many complex diseases. Analyzing single point mutations in a protein is crucial to see their impact and to understand the disease mechanism. This has given many biophysical resources, including databases and web-based tools to explore the effects of mutations on the structure and function of human proteins. For a given mutation, each tool provides a score-based outcomes which indicate deleterious probability. In recent years, developments in existing programs and the introduction of new prediction algorithms have transformed the state-of-the-art protein mutation analysis. In this study, we have performed a systematic study of the most commonly used mutational analysis programs (10 sequence-based and 5 structure-based) to compare their prediction efficiency. We have carried out extensive mutational analyses using these tools for previously known pathogenic single point mutations of five different proteins. These analyses suggested that sequence-based tools, PolyPhen2, PROVEAN, and PMut, and structure-based web tool, mCSM have a better prediction accuracy. This study indicates that the employment of more than one program based on different approaches should significantly improve the prediction power of the available methods. |
format | Online Article Text |
id | pubmed-9067658 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-90676582022-05-05 Comparative analysis of web-based programs for single amino acid substitutions in proteins Choudhury, Arunabh Mohammad, Taj Anjum, Farah Shafie, Alaa Singh, Indrakant K. Abdullaev, Bekhzod Pasupuleti, Visweswara Rao Adnan, Mohd Yadav, Dharmendra Kumar Hassan, Md. Imtaiyaz PLoS One Research Article Single amino-acid substitution in a protein affects its structure and function. These changes are the primary reasons for the advent of many complex diseases. Analyzing single point mutations in a protein is crucial to see their impact and to understand the disease mechanism. This has given many biophysical resources, including databases and web-based tools to explore the effects of mutations on the structure and function of human proteins. For a given mutation, each tool provides a score-based outcomes which indicate deleterious probability. In recent years, developments in existing programs and the introduction of new prediction algorithms have transformed the state-of-the-art protein mutation analysis. In this study, we have performed a systematic study of the most commonly used mutational analysis programs (10 sequence-based and 5 structure-based) to compare their prediction efficiency. We have carried out extensive mutational analyses using these tools for previously known pathogenic single point mutations of five different proteins. These analyses suggested that sequence-based tools, PolyPhen2, PROVEAN, and PMut, and structure-based web tool, mCSM have a better prediction accuracy. This study indicates that the employment of more than one program based on different approaches should significantly improve the prediction power of the available methods. Public Library of Science 2022-05-04 /pmc/articles/PMC9067658/ /pubmed/35507592 http://dx.doi.org/10.1371/journal.pone.0267084 Text en © 2022 Choudhury et al 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 use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Choudhury, Arunabh Mohammad, Taj Anjum, Farah Shafie, Alaa Singh, Indrakant K. Abdullaev, Bekhzod Pasupuleti, Visweswara Rao Adnan, Mohd Yadav, Dharmendra Kumar Hassan, Md. Imtaiyaz Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title | Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title_full | Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title_fullStr | Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title_full_unstemmed | Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title_short | Comparative analysis of web-based programs for single amino acid substitutions in proteins |
title_sort | comparative analysis of web-based programs for single amino acid substitutions in proteins |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9067658/ https://www.ncbi.nlm.nih.gov/pubmed/35507592 http://dx.doi.org/10.1371/journal.pone.0267084 |
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