In this book, I present an improved scatter search (SS) algorithm for predicting all-atoms protein structures using the CHARMM22 energy model. My algorithm produces a 3D structure of the whole protein by minimizing the energy function linked to protein folding. This is based on a sequence of amino acids as well as on data collected from known protein structures for comparative purposes. Defined as an evolutionary algorithm, SS relies on a population of candidate solutions. Candidate solutions, over a number of iterations, experience evolutionary operations which combine intense...