TCBG Seminar

Computer Prediction of Protein Docking and Analysis of Binding Interfaces

Dr. Julie C. Mitchell
Mathematics and Biochemistry
University of Wisconsin-Madison
Madison, WI

Monday, May 3, 2004
3:00 pm (CT)
3269 Beckman Institute


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 calculations.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.

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