GPU-based Cloud computing for comparing the structure of protein binding sites

In this paper, we present a novel approach for using a GPU-based Cloud computing infrastructure to efficiently perform a structural comparison of protein binding sites. The original CPU-based Java version of a recent graph-based algorithm called SEGA has been rewritten in OpenCL to run on NVIDIA GPUs in parallel on a set of Amazon EC2 Cluster GPU Instances. This new implementation of SEGA has been tested on a subset of protein structure data contained in the CavBase, providing a structural comparison of protein binding sites on a much larger scale than in previous research efforts reported in the literature.