SFLADock: A Memetic Protein-Protein Docking Algorithm

Protein-protein interactions are biologically significant as they govern many biological systems, including the immune and digestive systems. An abnormal increase in proteins may causes diseases like Alzheimer's disease, for which no cure is found yet. An advanced scientific study on their interactions and functions may shed light on the ways for treating protein-related diseases. Protein-protein docking is a method to study the structure of protein assemblies and hence their functions and characteristics. The proposed method uses the shuffled frog-leaping algorithm to predict the structure of protein complexes. Unlike other evolutionary algorithms that allow the use of information from previous generations only, this algorithm supports the use of all the information available at the moment. The division of the population into memeplexes and submemeplexes allows the searching for optimal solutions in different directions, thereby avoiding premature convergence. The proposed method is tested on the Docking Benchmark v 5. Results show that the method is capable of generating plausible structures of medium and acceptable quality even in the top 10 ranks. It should be noted that the results are independent of the initial position of individual proteins. The use of DFIRE scoring function to rank the poses helps in better throughput. The inclusion of a better selection strategy for conformations may positively change the results of the proposed method.