Molecular modeling:

A technique for the investigation of molecular structures and properties using computational chemistry and graphical visualization techniques in order to provide a plausible three- dimensional representation under a given set of circumstances. IUPAC Medicinal Chemistry

in silico: Literally "in the computer" (as contrasted with "in vitro" (in glass) or "in vivo" (in life). Can be used to screen out compounds which are not druggable.

Mapping and modeling networks and pathwaysThe experimental task of mapping genetic regulatory networks using genetic footprinting and [yeast] two- hybrid techniques is well underway, and the kinetics of these networks is being generated at an astounding rate. ... If the promise of the genome projects and the structural genomics effort is to be fully realized, then predictive simulation methods must be developed to make sense of this emerging experimental data.

There are three bottlenecks in the numerical analysis of biochemical reaction networks. The first is the multiple time scales involved. Since the time between biochemical reactions decreases exponentially with the total probability of a reaction per unit time, the number of computational steps to simulate a unit of biological time increases roughly exponentially as reactions are added to the system or rate constants are increased. The second bottleneck derives from the necessity to collect sufficient statistics from many runs of the Monte- Carlo simulation to predict the phenomenon of interest. The third bottleneck is a practical one of model building and testing: hypothesis exploration, sensitivity analyses, and back calculations, will also be computationally intensive.