How Flexible your Rigid-Body Docking Should Be

Carlos J. Camacho, Boston University.
 

I will discuss the feasibility of structural refinement in the context of protein-protein docking, emphasizing the benefits/disadvantages of backbone and side chain flexibility. I will mention the biophysical motivation for addressing the side chain refinement problem, and suggest how to solve it. Examples from blind predictions in the CAPRI experiment will also be mentioned.