Accelerating the Prediction of Protein Interactions

Slide Link

Alex Rodionov,  Jonathan Rose, Elisabeth R.M. Tillier and Alexandr Bezginov

Department of Electrical and Computer Engineering, and Department of Medical Biophysics and Ontario Cancer Institute, University of Toronto

October, 2010

Proteins are the building blocks of all living organisms, and studying  protein interactions helps us understand how life works. Lab experiments  and computer simulations of protein interactions are expensive, so it is advantageous to predict ahead of time which protein pairs are likely to  interact at all, before undertaking detailed experiments. 

This talk will be about my current Masters thesis, which is an interdisciplinary effort involving biology, software, and FPGA hardware design. Our collaborators at the Department of Medical Biophysics have developed a new method called MatrixMatchMaker (MMM) for predicting protein interactions by looking for a phenomenon called co-evolution  between pairs of proteins. I will describe MMM and our work in accelerating the original MMM algorithm using a combination of algorithmic and software optimization, and ongoing work in hardware acceleration.