Parallel CUDA-based protein 3D structure similarity searching

Finding common molecular substructures in complex 3D protein structures is still challenging. This is especially visible when scanning entire databases containing tens or even hundreds of thousands protein structures. Graphics processing units (GPUs) and general purpose graphics processing units (GPGPUs) promise to give a high speedup of many time-consuming and computationally demanding processes over their original implementations on CPUs. In this chapter, we will see that a massive parallelization of the 3D structure similarity searching on many core CUDA-enabled GPU devices leads to reduction of the execution time of the process and allows to perform it in real time.