Title:Functional Dynamics of Proteins Elucidated by Statistical Analysis of Simulation Data
Volume: 2
Issue: 4
Author(s): Burak Alakent, Zeynep Kurkcuoglu and Pemra Doruker
Affiliation:
Keywords:
Collective motions, Ligand binding, Nonlinear dynamics, Principal component analysis, Time series model,
Molecular dynamics simulations
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.
