Abstract

DOCKING SOFTWARE FOR MEMBRANE PROTEIN-LIGAND INTERACTIONS: A COMPARATIVE REVIEW

Saurabh Upadhayay, Shubhankit Soni*, Dr. Alok Shukla and Nitin Rajan

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Abstract

Protein-ligand interactions are essential for signal transduction, immune responses, and gene regulation. Understanding these interactions is crucial for deciphering biological regulation and for the development of new drug targets. In our study, we analyzed the molecular interactions between proteins and ligands that were docked using AutoDock 4.2 software. We employed a novel search algorithm, the Hybrid Algorithm of Random Drift Particle Swarm Optimization and Local Search (LRDPSO), in addition to the classical Lamarckian Genetic Algorithm (LGA) for energy optimization within AutoDock 4.2. The best conformations resulting from each docking algorithm were subjected to molecular dynamics (MD) simulations, allowing for a deeper exploration of the molecular mechanisms underlying proteinligand interactions. We focused on assessing the binding energy between protein receptors and ligands, the presence of salt bridges and hydrogen bonds within the docking region, as well as structural changes during complex unfolding. Comparing the complexes generated by these two docking methods, we found disparities in the protein-ligand interactions. This analysis underscored the significant roles played by salt bridge and hydrogen bond interactions in maintaining the stability of proteinligand complexes. Our study is primarily centered on isolating the deterministic characteristics of docking interactions from their dynamic properties, an essential step in comprehending biological functions and identifying amino acid residues critical to these interactions.

Keywords: Protein-ligand interactions, Signal transduction, Immune responses, Gene regulation, Molecular interactions, Docking.