A biased random key genetic algorithm for the protein-ligand docking problem

摘要

Molecular docking is a valuable tool for drug discovery. Receptor and flexible Ligand docking is a very computationally expensive process due to a large number of degrees of freedom of the ligand and the roughness of the molecular binding search space. A molecular docking simulation starts with receptor and ligand unbound structures, and the algorithm tests hundreds of thousands of ligand conformations and orientations to find the best receptor-ligand binding affinity by assigning and optimizing an energy function. Although the advances in the conception of methods and computational strategies for searching the best protein-ligand binding affinity, the development of new strategies, the adaptation, and investigation of new approaches and the combination of existing and state-of-the-art computational methods and techniques to the molecular docking problem are needed. We developed a Biased Random Key Genetic Algorithm as a sampling strategy to search the protein-ligand conformational space. We use a different method to discretize the search space. The proposed method (namely, BRKGA-DOCK) has been tested on a selection of protein-ligand complexes and compared to existing tools AUTODOCK VINA, DOCKTHOR, and a multiobjective approach (jMETAL). Compared to other traditional docking software, the proposed method shows best average Root-Mean-Square Deviation. Structural results were also statistically analyzed. The proposed method proved to be efficient and a good alternative for the molecular docking problem.