Minimum Population Search, an Application to Molecular Docking

Abstract

Computer modeling of protein-ligand interactions is one of the most important phases in a drug design process. Part of the process involves the optimization of highly multi-modal objective (scoring) functions. This research presents the Minimum Population Search heuristic as an alternative for solving these global unconstrained optimization problems. To determine the effectiveness of Minimum Population Search, a comparison with seven state-of-the-art search heuristics is performed. Being specifically designed for the optimization of large scale multi-modal problems, Minimum Population Search achieves excellent results on all of the tested complexes, especially when the amount of available function evaluations is strongly reduced. A first step is also made toward the design of hybrid algorithms based on the exploratory power of Minimum Population Search. Computational results show that hybridization leads to a further improvement in performance.

Keywords

• Minimum Population Search
• Molecular Docking
• Heuristic Algorithms
• Optimization
• Multi-modality