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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...

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Autores principales: Choudhury, Arunabh, Mohammad, Taj, Anjum, Farah, Shafie, Alaa, Singh, Indrakant K., Abdullaev, Bekhzod, Pasupuleti, Visweswara Rao, Adnan, Mohd, Yadav, Dharmendra Kumar, Hassan, Md. Imtaiyaz
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
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.
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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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