On the electrostatic component of protein-protein binding free energy.

ABSTRACT: Calculations of electrostatic properties of protein-protein complexes are usually done within framework of a model with a certain set of parameters. In this paper we present a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (DeltaDeltaGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius). The study was done using the largest so far set of entries comprising 260 hetero and 2148 homo protein-protein complexes extracted from a previously developed database of protein complexes (ProtCom). To test the sensitivity of the energy calculations with respect to the structural details

SUBMITTER: Talley K 

PROVIDER: S-EPMC2666630 | biostudies-literature | 2008 Nov

REPOSITORIES: biostudies-literature