Published Paper Details:

The basic building blocks of proteins, amino acids, have dynamic conformational flexibility that has a big impact on biological structure and function with small molecules can modulate these conformations, leading to altered biochemical behavior with implications in drug design, enzymatic regulation, and molecular recognition. This review presents a comprehensive computational investigation into the conformational changes of amino acids induced by small molecule interactions. Utilizing molecular dynamics (MD) simulations, quantum mechanical (QM) calculations, and hybrid QM/MM approaches, we explore how non-covalent interactions--such as hydrogen bonding, ?-? stacking, and van der Waals forces--affect the torsional angles and side-chain orientations of amino acids in isolated and solvated environments. Emphasis is placed on the role of solvent effects, energy landscapes, and potential energy surface (PES) mapping in elucidating these conformational shifts. Case studies involving biologically relevant ligands demonstrate the diverse effects of small molecules on the structural plasticity of amino acids. By integrating data from recent computational studies, this review highlights emerging trends, methodological advancements, and key challenges in the field. The findings provide critical insights for rational drug design, peptide engineering, and understanding protein-ligand interactions at the molecular level.