Simbios Talk by Patrice Koehl, University of California Davis, January 17, 2007

Title: Geometry for Biomolecules

The molecular basis of life rests on the activity of biological macro-molecules, mostly nucleic acids and proteins.  A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities.  In this seminar, I address this connection between biology and geometry.
More specifically, in the first part of the talk, I will show how simple geometric calculations can help us understand solvation, as well as residue accessibility in macromolecules measured by footprinting experiments.

Electrostatics calculations remain computationally intensive and difficult to set up. There is therefore a need for a comprehensive toolkit for computing macromolecular electrostatics that would be freely available, easy to interface with other applications, and available as a web service to allow non specialists to perform these types of calculation. In the second part of this talk, I will present our recent developments of such a toolkit that will be integral part of SimTK.