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Accurate estimation of free energy differences has enormous applications, from understanding a fundamental biochemical process to rational drug design. Statistical mechanics based approaches, such as alchemical free energy calculations, are proven to be highly accurate in calculating the free energy difference between two chemically well-defined states. In this webinar, I will provide an overview of calculating free energy change due to protein mutation using the open-source PMX software and web server. I will also show results from large-scale alchemical calculations of relative and absolute binding free energy for protein-ligand systems. In the end, a brief overview of the ongoing development in PMX will be presented.


Sudarshan Behera is a postdoctoral researcher in the Computational Biomolecular Dynamics group at the Max Planck Institute for Multidisciplinary Sciences, Goettingen. He is involved in developing methods for identifying and tackling convergence issues in non-equilibrium alchemical free energy calculations, as well as in the development of PMX software. Prior to this, whilst studying for his Ph.D. at JNCASR, Bangalore, India, he investigated the structure and dynamics of various enzymes using MD and enhanced sampling methods.