Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods

Entropy of binding constitutes a major, and in many cases a detrimental, component of the binding affinity in biomolecular interactions. While the enthalpic part of the binding free energy is easier to calculate, estimating the entropy of binding is further more complicated. A precise evaluation of entropy requires a comprehensive exploration of the complete phase space of the interacting entities. As this task is extremely hard to accomplish in the context of conventional molecular simulations, calculating entropy has involved many approximations. Most of these golden standard methods focused on developing a reliable estimation of the conformational part of the entropy. Here, we review these methods with a particular emphasis on the different techniques that extract entropy from atomic fluctuations. The theoretical formalisms behind each method is explained highlighting its strengths as well as its limitations, followed by a description of a number of case studies for each method. We hope that this brief, yet comprehensive, review provides a useful tool to understand these methods and realize the practical issues that may arise in such calculations.