Protein structure refinement with a memetic algorithm

Abstract

A memetic approach to protein structure refinement was defined, combining Differential Evolution and the widely used Rosetta Relax refinement protocol. This refinement process can be considered as an optimization problem to optimize the positions of the amino acid atoms of the protein. The local optimization procedures of Rosetta Relax are integrated into the evolutionary algorithm. The results with different proteins show that the memetic algorithm better samples the energy landscape compared to Rosetta Relax, obtaining better energy-optimized refined conformations in the same runtime.