Dr. Ryan Brenke
rbrenke [at] bu [dot] edu
The goal of my research is to improve protein-protein docking and computational solvent mapping methodologies. To this end, we have developed an FFT based protein-protein docking prediction program (Piper) that uses a novel knowledge-based energy scoring function.
Our lab has been using Piper in the international protein-protein docking prediction experiment, CAPRI, with great success.
In order to provide the docking community with access to our docking tools, we have developed a server, ClusPro, that uses Piper as an initial stage docking algorithm and then a clustering algorithm to produce a few predicted models for a given pair of receptor and ligand proteins.
I am also working on the development of a computational solvent mapping algorithm to attempt to model the results of experimental solvent mapping methods such as the MSCS (multiple solvent crystal structures) method developed by Carla Mattos and Dagmar Ringe. This algorithm uses many of the same principles used in Piper (i.e. FFT based correlation sampling), but also incorporates numerous changes to the program and its energy functions. We plan to develop a server to host this application as well.