ABSTRACT
This chapter briefly introduces the main aspects of the Protein Folding Problem and presents a reviews of the related works. It presents an overview of the Multi-Objective optimization context and the Non-dominated Sorting Genetic Algorithm (NSGA-II) and Indicator-Based Algorithm (IBEA) algorithms are presented. The chapter presents the experimental benchmark and numerical results of the conducted experiments. It investigates the distance because more compact structures tend to have more hydrophobic contacts: as the lower the Euclidean distance between the amino acids is, the more compact the whole conformation will be. The prediction of protein structures has a wide range of important biotechnological and medical applications, e.g., design of new proteins and folds, structure-based drug design, and obtaining experimental structures from incomplete nuclear magnetic resonance data. The protein structures are the result of the so-called protein folding process in which the initially unfolded chain of amino acids is transformed into its final structure.
