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

Abstract

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.

Integration of in vitro and in-silico analysis of Caulerpa racemosa against antioxidant, antidiabetic, and anticancer activities

“…RasWin software was used to visualize the ligand structure. The ligand was prepared for docking by adding Gasteiger charges and saved in PDBQT format 44 .…”

In silico study of SARS‐CoV‐2 spike protein RBD and human ACE‐2 affinity dynamics across variants and Omicron subvariants

“… 26 The development of novel drugs primarily focuses on the interaction interface. 27 A mutation at a particular site or interface may directly impact binding and expression. Therefore, identifying specific protein binding aids in developing novel therapeutic strategies, particularly considering the relationship between the spike glycoprotein's RBD and the hACE2R.…”

“…The mutations in the SP could enhance the viral entry into the host cell, and the RBD could affect viral infectivity and stability 26 . The development of novel drugs primarily focuses on the interaction interface 27 . A mutation at a particular site or interface may directly impact binding and expression.…”

cLD: Rare-variant linkage disequilibrium between genomic regions identifies novel genomic interactions

“…HDOCKlite-v1.1 [ 25 , 26 ] was employed for conducting the protein-protein docking analysis between the cLD prioritized protein pairs ( Section 4 in S1 Text ). The protein’s crystal structure was obtained from the Protein Data Bank [ 27 ] and further validated [ 28 ] ( Section 4.1 in S1 Text ). The output file of the docked complex was visualized by PyMOL 2.5.1 [ 29 ], and the 2D plot of the protein-protein binding region was analyzed and deduced using LigPlot+ v.2.2 [ 30 ] ( Section 4.2 in S1 Text ).…”