Protein structure prediction in an atomic model with differential evolution integrated with the crowding niching method

A hybrid version between differential evolution and the fragment replacement technique was defined for protein structure prediction. The coarse-grained atomic model of the Rosetta system was used for protein representation. The high-dimensional and multimodal nature of protein energy landscapes requires an efficient search for obtaining the native structures with minimum energy. However, the energy model of Rosetta presents an additional difficulty, since the best energy area in the landscape does not necessarily correspond to the closest conformations to the native structure. A strategy is to obtain a diverse set of protein conformations that correspond to different minima in the landscape. The incorporation of the crowding niching method into the hybrid evolutionary algorithm allows addressing the problem of the energy landscape deceptiveness, allowing to obtain a set of optimized and diverse protein folds.

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