Computer Prediction of Protein Docking and Analysis of Binding <br/><br/>Interfaces

Tuesday, April 12, 2005 - 9:30am - 10:30am
EE/CS 3-180
Julie Mitchell (University of Wisconsin, Madison)
Recent work on the development of methods for protein docking and
analysis of binding interfaces will be discussed. One of the methods
presented is the Docking Mesh Evaluator that uses an implicit solvent
model for electrostatics. The Docking Mesh Evaluator is capable of
exhaustive search as well as of local and global optimization of binding
energies, all of which can be performed using parallel computation.

The Fast Atomic Density Evaluator is a method for analyzing protein
shape, and shape complementarity within binding interfaces. The Fast
Atomic Density Evaluator's complementarity hot spots correlate with
residues in which mutation is known to impact binding. This has
recently been used in the development of engineered ribonucleases able
to kill cancer cells. Shape complementarity analysis can also aid
docking prediction, either as a post-filter for exhaustive search
results or as a means of dynamic parameterization for flexible docking