5. Molecular Modeling in Biochemistry

D.R. Bevan

The CAVE facility will greatly increase our capabilities in molecular modeling both in research and teaching. Dr. Bevan's current research projects, in which molecular modeling is applied, include: 1. structural analysis and visualization of proteins, 2. simulation of distance distributions in peptides, 3. solvation energies and their relationship to membrane permeability, and 3. isomerization of proline-containing peptide bonds.

The aspects of these projects that involve visualization of structures will be greatly enhanced by the ability to view the molecules in a CAVE. A CAVE also will provide the environment to gain a better "feel" for molecular interactions through the tactile responses that are possible. Dr. Bevan also teaches courses in which the CAVE will be used and he assists other biochemistry faculty who want to apply structure visualization in teaching. For example, Dr. Bevan has taught several times a graduate-level course entitled "Molecular Modeling of Proteins and Nucleic Acids." Students learn the theory of molecular modeling, but much of the course is taught from from a more practical perspective in that students are required to do several computer-based problems and projects. The students in the molecular modeling course will all experience the CAVE for visualization, and those with the inclination will apply it in their class projects.

The Department of Biochemistry has the second or third largest undergraduate enrollment in the country. Dr. Bevan will use the CAVE to assist these students in visualizing protein and nucleic acid structures as part of their undergraduate training. Many years ago when we first began using computer visualization of structures in our classes, the students were very enthusiastic because they gained a much better understanding of structural features. The CAVE will raise this educational experience to a level that far surpasses what we are currently able to provide.