Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.

ABSTRACT: Macromolecular interactions are essential for understanding numerous biological processes and are typically characterized by the binding free energy. Important component of the binding free energy is the electrostatics, which is frequently modeled via the solutions of the Poisson-Boltzmann Equations (PBE). However, numerous works have shown that the electrostatic component (ΔΔGelec ) of binding free energy is very sensitive to the parameters used and modeling protocol. This prompted some researchers to question the robustness of PBE in predicting ΔΔGelec . We argue that the sensitivity of the absolute ΔΔGelec calculated with PBE using different input parameters and definitions does not indicate PBE deficiency, rather this is what should be expected. We show how the apparent sensitivity sho

SUBMITTER: Chakavorty A 

PROVIDER: S-EPMC5030180 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature