Visualization of Molecules with Positional Uncertainty

Abstract

Designing new and better chemotherapeutic wmpounds requires an understanding of the mechanism by which the drugs exert their biological effects. This involves consideration of the geometry of the active site, determination of the geometry of the drug, and analysis of the fit between them. This problem of dr ug-suhstrate fit . often called the docking problem, can he greatly in fluenced by uncertainty in the position of drug side chains. Tradit ional molecular graphics techniques fail to capture the dist ribution oflikely atom positions. This paper describes a range of tedmiques for showing atom positions as probability distributions that more completely describe parameters which determine fit.