UNIT 8.3 Evaluation of Electrostatic Interactions
Published Online: 1 AUG 2003
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
How to Cite
Green, D. F. and Tidor, B. 2003. Evaluation of Electrostatic Interactions. Current Protocols in Bioinformatics. 2:8.3:8.3.1–8.3.16.
- Published Online: 1 AUG 2003
- Published Print: MAY 2003
Described here are several computational procedures for the analysis of electrostatic interactions in molecular complexes, all based on a continuum model of solvation. The first section describes how to compute the residual potential, a measure of how electrostatically complementary a ligand is for its receptor. The second procedure describes electrostatic component analysis, a method by which the electrostatic contribution to the binding free energy can be broken up into terms directly attributable to individual chemical groups. Finally, electrostatic affinity optimization is described. This procedure is particularly useful in determining what portions of a ligand are the most suboptimal, and thus provide the greatest opportunity for the design of improvements.