A GPU-Based Approach to Accelerate Computational Protein-DNA Docking

This article describes a GPU-based high-performance computing method to tackle the protein-DNA docking problem. GPU-specific algorithmic techniques are developed to accelerate a docking algorithm that integrates Monte Carlo simulation and simulated annealing. Experiments show that such improved computation speed accelerates the conformational space sampling of the algorithm and increases the chance of finding near-native protein-DNA structures.