Evolutionary algorithm for predicting all-atom protein structure

Abstract

We present an improved version of a scatter search (SS) algorithm for predicting all-atoms protein structures using a recent energy model. This algorithm produces a 3D structure of the whole protein, including back-bone and side-chain atoms, by minimizing the energy function associated with the structure. We evaluate our algorithm on proteins taken from a Protein Data Bank. Our results show that our algorithm produces promising 3D structures and demonstrates the advantage of the energy model used.