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

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

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Abstract

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.

Item Type:	Article
Keyword:	Protein , Amino acid substitution , Computational biology
Subjects:	Q Science > QA Mathematics > QA1-939 Mathematics > QA71-90 Instruments and machines > QA75.5-76.95 Electronic computers. Computer science > QA76.75-76.765 Computer software Q Science > QP Physiology > QP1-(981) Physiology
Department:	FACULTY > Faculty of Medicine and Health Sciences
Depositing User:	SAFRUDIN BIN DARUN -
Date Deposited:	30 Sep 2022 18:52
Last Modified:	30 Sep 2022 18:52
URI:	https://eprints.ums.edu.my/id/eprint/34177

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