A survey of computational treatments of biomolecules by robotics-inspired methods modeling equilibrium structure and dynamics

Abstract

More than fifty years of research in molecular biology have demonstrated that the ability of small and large molecules to interact with one another and propagate the cellular processes in the living cell lies in the ability of these molecules to assume and switch between specific structures under physiological conditions. Elucidating biomolecular structure and dynamics at equilibrium is therefore fundamental to furthering our understanding of biological function, molecular mechanisms in the cell, our own biology, disease, and disease treatments. By now, there is a wealth of methods designed to elucidate biomolecular structure and dynamics contributed from diverse scientific communities. In this survey, we focus on recent methods contributed from the Robotics community that promise to address outstanding challenges regarding the disparate length and time scales that characterize dynamic molecular processes in the cell. In particular, we survey robotics-inspired methods designed to obtain efficient representations of structure spaces of molecules in isolation or in assemblies for the purpose of characterizing equilibrium structure and dynamics. While an exhaustive review is an impossible endeavor, this survey balances the description of important algorithmic contributions with a critical discussion of outstanding computational challenges. The objective is to spur further research to address outstanding challenges in modeling equilibrium biomolecular structure and dynamics.