Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.

ABSTRACT: We present a thermodynamical approach to identify changes in macromolecular structure and dynamics in response to perturbations such as mutations or ligand binding, using an expansion of the Kullback-Leibler Divergence that connects local population shifts in torsion angles to changes in the free energy landscape of the protein. While the Kullback-Leibler Divergence is a known formula from information theory, the novelty and power of our implementation lies in its formal developments, connection to thermodynamics, statistical filtering, ease of visualization of results, and extendability by adding higher-order terms. We present a formal derivation of the Kullback-Leibler Divergence expansion and then apply our method at a first-order approximation to molecular dynamics simulations of four

SUBMITTER: McClendon CL 

PROVIDER: S-EPMC3538811 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature