Evaluation of electrostatic interactions.
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.
Green
David F
DF
Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Tidor
Bruce
B
D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D004563:Electrochemistry / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D055672:Static Electricity
D011506:Proteins