The MidasPlus molecular modeling system

MidasPlus [6, 7] is an interactive molecular modeling system used to depict three dimensional macromolecular structures such as proteins and nucleic acids, to study how these structures spatially and chemically interact, and to study how small molecules such as drugs bind with these macromolecules, Effective interaction with macromolecular structures presents several challenges: the molecules consist of thousands to tens of thousands of atoms and the scientist user is easily overwhelmed by the sheer volume of data if the displayed information is not limitied and presented in a rational manner. The intellectual process of understanding the structure and function of molecules is linked to visualizing the complex spatial relationships within these structures, and since the user ia only presented images of models, this intellectual process must proceed without being able to physically handle and make experimental “hand driven” modifications of a physical model. Finally, macromolecules are often globular in shape, of course bear no resemblance to macroscopic physical objects in the real world, and hence make it inherently difficult for the human visual system to accurately perceive the complex spatial relationships that are ao crucial to chemical activity.