title: Screened charge electrostatic model in protein-protein docking simulations.
abstract: 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.
authors.affiliation: Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jfrecio@scripps.edu
authors.forename: Juan
authors.initials: J
authors.lastname: Fernandez-Recio
authors.forename: Maxim
authors.initials: M
authors.lastname: Totrov
authors.forename: Ruben
authors.initials: R
authors.lastname: Abagyan
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012996:Solutions; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D004798:Enzymes; D011506:Proteins; D012996:Solutions