Packing protein side-chains by parallel ant colonies

Side-chains are crucial for proteins expressing their biochemical characteristics. Packing protein side-chains is then a necessary task for protein structure prediction, and critical to some descendant and important applications, such as protein design, docking and point mutation analysis. Given all possible candidate rotamers for each residue of protein backbone, packing protein side-chains can be modeled as a combinatorial optimization problem without an accurate energy function. This paper presents a parallel approach, pacoPacker, to pack protein side-chains by ant colony optimization. Each ant colony is used to pack side-chains with the guidance of an energy function. Different colonies use different energy functions. These multiple colonies are running in parallel and cooperate with each other by sharing the pheromone matrix whose role is to tune sampling the rotamer library. In this way, the intelligences embedded in different energy functions can be brought together to find out the best side-chains for the protein backbone. Experimental study has been conducted on two typical benchmarks, and the results show that pacoPacker is competitive to the state-of-art systems.