Drug Design Issues on the Cell BE

Structure alignment prediction between proteins (protein docking) is crucial for drug design, and a challenging problem for bioinformatics, pharmaceutics, and current and future processors due to it is a very time consuming process. Here, we analyze a well known protein docking application in the Bioinformatic field, Fourier Transform Docking (FTDock), on a 3.2GHz Cell Broadband Engine (BE) processor. FTDock is a geometry complementary approximation of the protein docking problem, and baseline of several protein docking algorithms currently used. In particular, we measure the performance impact of reducing, tuning and overlapping memory accesses, and the efficiency of different parallelization strategies (SIMD, MPI, OpenMP, etc.) on porting that biomedical application to the Cell BE. Results show the potential of the Cell BE processor for drug design applications, but also that there are important memory and computer architecture aspects that should be considered.