Visualization of Molecules with Positional Uncertainty

Designing new and better chemotherapeutic compounds 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 drug-substrate fit, often called the docking problem, can be greatly influenced by uncertainty in the position of drug side chains. Traditional molecular graphics techniques fail to capture the distribution of likely atom positions. This paper describes a range of techniques for showing atom positions as probability distributions that more completely describe parameters which determine fit. ...