Abstract

Conformational dynamics and flexibility form the link between protein structure and function. Molecular dynamics (MD) simulations have been valuable for our understanding of conformational energy landscape and protein dynamics at the atomic scale, which is difficult to probe experimentally. In this respect, the essential dynamics of proteins revealed by principal component analysis of MD simulation data provide information on functional motions that generally bear a collective nature. In this review, we summarize literature on statistical analysis of MD data with an emphasis on recent promising methods that can be applied to study the effect of ligand binding.

Keywords: Collective motions, Ligand binding, Nonlinear dynamics, Principal component analysis, Time series model, Molecular dynamics simulations