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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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Main Authors:	Arunabh Choudhury, Taj Mohammad, Farah Anjum, Alaa Shafie, Indrakant K. Singh, Bekhzod Abdullaev, Pasupuleti Visweswara Rao, Mohd Adnan, Dharmendra Kumar Yadav, Md. Imtaiyaz Hassan
Format:	Article
Language:	English English
Published:	Public Library Science 2022
Subjects:	QA76.75-76.765 Computer software QP1-(981) Physiology
Online Access:	https://eprints.ums.edu.my/id/eprint/34177/1/FULL%20TEXT.pdf https://eprints.ums.edu.my/id/eprint/34177/2/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/34177/ https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267084 https://doi.org/10.1371/journal.pone.0267084
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spelling	my.ums.eprints.341772022-09-30T10:52:39Z https://eprints.ums.edu.my/id/eprint/34177/ Comparative analysis of web-based programs for single amino acid substitutions in proteins Arunabh Choudhury Taj Mohammad Farah Anjum Alaa Shafie Indrakant K. Singh Bekhzod Abdullaev Pasupuleti Visweswara Rao Mohd Adnan Dharmendra Kumar Yadav Md. Imtaiyaz Hassan QA76.75-76.765 Computer software QP1-(981) Physiology 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 indicates 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 Science 2022 Article PeerReviewed text en https://eprints.ums.edu.my/id/eprint/34177/1/FULL%20TEXT.pdf text en https://eprints.ums.edu.my/id/eprint/34177/2/ABSTRACT.pdf Arunabh Choudhury and Taj Mohammad and Farah Anjum and Alaa Shafie and Indrakant K. Singh and Bekhzod Abdullaev and Pasupuleti Visweswara Rao and Mohd Adnan and Dharmendra Kumar Yadav and Md. Imtaiyaz Hassan (2022) Comparative analysis of web-based programs for single amino acid substitutions in proteins. PLoS ONE, 17. pp. 1-12. ISSN 1932-6203 https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267084 https://doi.org/10.1371/journal.pone.0267084
institution	Universiti Malaysia Sabah
building	UMS Library
collection	Institutional Repository
continent	Asia
country	Malaysia
content_provider	Universiti Malaysia Sabah
content_source	UMS Institutional Repository
url_provider	http://eprints.ums.edu.my/
language	English English
topic	QA76.75-76.765 Computer software QP1-(981) Physiology
spellingShingle	QA76.75-76.765 Computer software QP1-(981) Physiology Arunabh Choudhury Taj Mohammad Farah Anjum Alaa Shafie Indrakant K. Singh Bekhzod Abdullaev Pasupuleti Visweswara Rao Mohd Adnan Dharmendra Kumar Yadav Md. Imtaiyaz Hassan Comparative analysis of web-based programs for single amino acid substitutions in proteins
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 indicates 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	Article
author	Arunabh Choudhury Taj Mohammad Farah Anjum Alaa Shafie Indrakant K. Singh Bekhzod Abdullaev Pasupuleti Visweswara Rao Mohd Adnan Dharmendra Kumar Yadav Md. Imtaiyaz Hassan
author_facet	Arunabh Choudhury Taj Mohammad Farah Anjum Alaa Shafie Indrakant K. Singh Bekhzod Abdullaev Pasupuleti Visweswara Rao Mohd Adnan Dharmendra Kumar Yadav Md. Imtaiyaz Hassan
author_sort	Arunabh Choudhury
title	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_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_sort	comparative analysis of web-based programs for single amino acid substitutions in proteins
publisher	Public Library Science
publishDate	2022
url	https://eprints.ums.edu.my/id/eprint/34177/1/FULL%20TEXT.pdf https://eprints.ums.edu.my/id/eprint/34177/2/ABSTRACT.pdf https://eprints.ums.edu.my/id/eprint/34177/ https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0267084 https://doi.org/10.1371/journal.pone.0267084
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score	13.211869

Comparative analysis of web-based programs for single amino acid substitutions in proteins

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