Free Energy Landscape Analysis of Mesoscopic Model for Finding DNA-Protein Binding Sites

Abstract

The physical modelization of biomolecules requires a careful choice of the scale of work depending on the problem we wish to study. All-atom simulations allow an accurate description of the system but within small time scales and severe size limitations subject to the available computational power. Coarse-grained models gather groups of atoms in point particles simplifying greatly the system but keeping the essence of the important interactions in the problem of study. At this level, the free energy landscape (FEL) of the system appears as a powerful tool to extract relevant information from a system with a high number of degrees of freedom.