Gene-Gene Interaction Mapping Of Human Cytomegalic Virus through System Biology Approach

Saxena, Navrati; Saxena, Vijaylaxmi; Dixit, Supriya; Ashraf, Alfisha

doi:10.4172/2329-6577.1000141

Cited by 2 publications

(2 citation statements)

References 8 publications

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“…Some of these mechanisms can become clinically significant if compromised and can lead to disease conditions such as tumorigenesis. Therefore, the study of gene–gene interaction maps of model organisms and humans has been incorporated into drug discovery and design [ 75 ]. Gene interaction mapping of cathepsins B, L1, and S revealed several clinically compromised pathways caused by cathepsin overexpression ( Figure 11 ).…”

Section: Discussionmentioning

confidence: 99%

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

Perera

Peiris

2021

Biology

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Current in silico 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.

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Section: Discussionmentioning

confidence: 99%

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

Perera

Peiris

2021

Biology

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show abstract

“…Some of these mechanisms can become clinically significant if compromised and lead to disease conditions such as tumorigenesis. Therefore, the study of gene-gene interaction maps of model organisms and humans have been incorporated in drug discovery and design [51]. Gene interaction mapping of Cathepsins B, L1 and S revealed a number of clinically compromised pathways caused by Cathepsin overexpression (Fig.…”

Section: Had a Common Ancestry Between The Type 1 Cystatins Cystatinmentioning

confidence: 99%

A benchmarked in-silico driven pipeline capable of complete trifecta protein analysis

Perera¹,

Peiris²

2020

Preprint

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Background Current in-silico based proteomics requires the prediction, validation and functional analysis of a modelled protein. The main drawback in this protocol is the lack of a singular protocol that utilizes a proper set of benchmarked open science tools to accurately predict a protein’s structure and function. Results The present study aims to utilize a series of openly available computational tools to formulate a complete pipeline capable of analyzing a novel protein’s amino acid sequence, reveal its phylogenetic relationships and conserved residues. The resultant data would then be utilized in the formulation of the protein’s tertiary structure followed by functional analysis through virtual screening. This novel protocol was benchmarked utilizing the Cystatin C protein obtained from Danio rerio and the AChE proteins of Homo sapiens and Rattus norvegicus. Conclusion The resultant pipeline utilizes freely available in-silico tools capable of complete protein analysis including a novel protein’s functional analysis. The methodology has been proven and the tools have been benchmarked as the most suited for complete trifecta protein analysis.

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Gene-Gene Interaction Mapping Of Human Cytomegalic Virus through System Biology Approach

Cited by 2 publications

References 8 publications

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

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

A benchmarked in-silico driven pipeline capable of complete trifecta protein analysis

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