A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery

Current <i>in silico</i> proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of benchmarked open-source tools to predict a...

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Autores principales:	D. D. B. D. Perera, K. Minoli L. Perera, Dinithi C. Peiris
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	virtual screening therapeutic targets protein modulation trifecta analysis Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/5dd0874289dd4e2f8ac8e5d41d89ece3
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id	oai:doaj.org-article:5dd0874289dd4e2f8ac8e5d41d89ece3
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spelling	oai:doaj.org-article:5dd0874289dd4e2f8ac8e5d41d89ece32021-11-25T16:47:07ZA Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery10.3390/biology101111132079-7737https://doaj.org/article/5dd0874289dd4e2f8ac8e5d41d89ece32021-10-01T00:00:00Zhttps://www.mdpi.com/2079-7737/10/11/1113https://doaj.org/toc/2079-7737Current <i>in silico</i> proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of benchmarked open-source tools to predict a protein’s structure and function accurately. The present study rectifies this drawback through the design and development of such a protocol. The protocol begins with the characterization of a novel coding sequence to identify the expressed protein. It then recognizes and isolates evolutionarily conserved sequence motifs through phylogenetics. The next step is to predict the protein’s secondary structure, followed by the prediction, refinement, and validation of its three-dimensional tertiary structure. These steps enable the functional analysis of the macromolecule through protein docking, which facilitates the identification of the protein’s active site. Each of these steps is crucial for the complete characterization of the protein under study. We have dubbed this process the trifecta analysis. In this study, we have proven the effectiveness of our protocol using the cystatin C and AChE proteins. Beginning with just their sequences, we have characterized both proteins’ structures and functions, including identifying the cystatin C protein’s seven-residue active site and the AChE protein’s active-site gorge via protein–protein and protein–ligand docking, respectively. This process will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could expand drug development.D. D. B. D. PereraK. Minoli L. PereraDinithi C. PeirisMDPI AGarticlevirtual screeningtherapeutic targetsprotein modulationtrifecta analysisBiology (General)QH301-705.5ENBiology, Vol 10, Iss 1113, p 1113 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	virtual screening therapeutic targets protein modulation trifecta analysis Biology (General) QH301-705.5
spellingShingle	virtual screening therapeutic targets protein modulation trifecta analysis Biology (General) QH301-705.5 D. D. B. D. Perera K. Minoli L. Perera Dinithi C. Peiris A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
description	Current <i>in silico</i> proteomics require the trifecta analysis, namely, prediction, validation, and functional assessment of a modeled protein. The main drawback of this endeavor is the lack of a single protocol that utilizes a proper set of benchmarked open-source tools to predict a protein’s structure and function accurately. The present study rectifies this drawback through the design and development of such a protocol. The protocol begins with the characterization of a novel coding sequence to identify the expressed protein. It then recognizes and isolates evolutionarily conserved sequence motifs through phylogenetics. The next step is to predict the protein’s secondary structure, followed by the prediction, refinement, and validation of its three-dimensional tertiary structure. These steps enable the functional analysis of the macromolecule through protein docking, which facilitates the identification of the protein’s active site. Each of these steps is crucial for the complete characterization of the protein under study. We have dubbed this process the trifecta analysis. In this study, we have proven the effectiveness of our protocol using the cystatin C and AChE proteins. Beginning with just their sequences, we have characterized both proteins’ structures and functions, including identifying the cystatin C protein’s seven-residue active site and the AChE protein’s active-site gorge via protein–protein and protein–ligand docking, respectively. This process will greatly benefit new and experienced scientists alike in obtaining a strong understanding of the trifecta analysis, resulting in a domino effect that could expand drug development.
format	article
author	D. D. B. D. Perera K. Minoli L. Perera Dinithi C. Peiris
author_facet	D. D. B. D. Perera K. Minoli L. Perera Dinithi C. Peiris
author_sort	D. D. B. D. Perera
title	A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
title_short	A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
title_full	A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
title_fullStr	A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
title_full_unstemmed	A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery
title_sort	novel <i>in silico</i> benchmarked pipeline capable of complete protein analysis: a possible tool for potential drug discovery
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5dd0874289dd4e2f8ac8e5d41d89ece3
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A Novel <i>In Silico</i> Benchmarked Pipeline Capable of Complete Protein Analysis: A Possible Tool for Potential Drug Discovery

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