Summary Physical stability is a key determinant of the clinical and commercial success of biological therapeutics, vaccines, diagnostics, enzymes, and other protein-based products. The development of accurate computational methods for predicting protein stability can reduce the cost and time of experimental mutant design campaigns. In this work, we demonstrate the success of a rigorous physics-based computational method, Free Energy Perturbation (FEP), at quantitatively evaluating the relative thermodynamic stability of a diverse set of proteins on a dataset consisting of 328 single point mutations spread across 14 distinct protein structures and we will discuss the effects of simulation conditions on the computational predictions.
