Screened charge electrostatic model in protein-protein docking simulations.

A new method for considering solvation when calculating electrostatics for protein docking is proposed. The solvent-exposed charges are attenuated by induced solvent polarization charges. Modified charges are pre-calculated and the correction doesn't affect the speed of the actual simulation. The new Screened Charge Electrostatic Model (SChEM) results in an improved discrimination of near-native solutions from false positives in docking simulations as compared to conventional 'non-solvated' charge assignment. A series of protein-protein complexes were analyzed by running automated rigid-body Monte-Carlo docking simulations using the 3-D coordinates of the unbound components. In all but one case, the use of solvation screened charges for electrostatic calculations helped to improve the rank of the near-native solution after rigid-body simulations. The SChEM also drastically improved the results of the subsequent refinement of the interface side-chains. In all cases the final lowest energy solution was found within 3.0 A r.m.s.d. of the crystal structure.