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A Memetic Algorithm for Protein Structure Prediction based on the 2D Triangular Lattice Model

Proteins play fundamental and crucial roles in nearly all biological processes, such as, enzymatic catalysis, signaling transduction, embryonic development, and DNA and RNA synthesis. The main function of the protein is decided by its structure. Therefore, many researchers are interested in the prediction of protein structure. The HP model is one of the commonly used models. But most research on the HP lattice model focuses on how to solve the problem of optimization and ignores the purpose of protein structure prediction, namely the prediction of structure similarity between proteins. The 2D triangular lattice model used in this study can predicate protein structure more closely to its topology compared to the 2D square model commonly used in the past. Besides proposing an effective memetic algorithm (MA), this study also investigated structure similarity of natural proteins.