PARALLEL-PROBIS: FAST PARALLEL ALGORITHM FOR LOCAL STRUCTURAL COMPARISON OF PROTEIN STRUCTURES AND BINDING SITES
Presented by Ms. Kati ROZMAN
Type: Oral presentation
We present a new parallelized algorithm, Parallel-ProBiS, for detecting similar binding sites on clusters of computers. This is a new algorithm that calcu- lates the local similarity metric between protein structures, and is especially suited to efficient execution on multiple CPUs. The obtained speedups of the parallel ProBiS scale almost ideally with the number of computing cores up to about 64 computing cores. Scaling is better for larger than for smaller query proteins. For a protein with almost 600 amino acids, the maximum speedup of 180 was achieved on two interconnected clusters with 248 computing cores. Source code of Parallel-ProBiS is available for download free for academic users at http://probis.cmm.ki.si/download.