Simulation of enzyme-substrate interactions: the diffusional encounter step.

Enzymes are targets for structure-based redesign and drug design. One potentially important design strategy is to create molecules--enzymes and ligands--with desired diffusional encounter properties. Rates of diffusive bimolecular encounter can be calculated by Brownian dynamics simulation. This methodology and its application to study the factors influencing the rates of diffusion-influenced enzymes are described here.