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Summary: 1
SCREENED CHARGE ELECTROSTATIC MODEL IN
PROTEIN-PROTEIN DOCKING SIMULATIONS
JUAN FERNANDEZ-RECIO1
, MAXIM TOTROV2
, RUBEN ABAGYAN1
1
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey
Pines Road, La Jolla, CA 92037,USA, E-mail: jfrecio@scripps.edu, abagyan@scripps.edu
2
Molsoft, LLC, 3366 Torrey Pines Court, La Jolla, CA 92037, USA,
E-mail: totrov@molsoft.com
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
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