Published Paper Details:

This study investigates the dynamic behavior and stability of proteins and protein-ligand complexes through molecular dynamics (MD) simulations using the Desmond Molecular Dynamics system and the OPLS 2005 all-atom force field. The simulations aimed to explore the conformational changes, fluctuations, and overall stability of proteins in both their unbound forms and when complexed with ligands over a 10-nanosecond period. To assess the binding affinity and energetics of the protein-ligand complexes, the Prime/MM-GBSA method was employed, which calculates the binding free energies (?G binding) by considering various energy components, including the energy of the complex, solvation energy difference, and surface area energy difference. The study utilized the OPLS-AA force field and the GB/SA continuum solvent model to estimate the binding free energies, providing insights into the stability and strength of the receptor-ligand interactions, which are crucial for identifying potential drug candidates and optimizing ligands for enhanced binding affinity.