Evolving L-systems to capture protein structure native conformations

Abstract

A protein is a linear chain of amino acids that folds into a unique functional structure, called its native state. In this state, proteins show repeated sub-structures like alpha helices and beta sheets. This suggests that native structures may be captured by the formalism known as Lindenmayer systems (L-systems). In this paper an evolutionary approach is used as the inference procedure for folded structures on simple lattice models. The algorithm searches the space of L-systems which are then executed to obtain the phenotype, thus our approach is close to Grammatical Evolution. The problem is to find a set of rewriting rules that represents a target native structure on the lattice model. The proposed approach has produced promising results for short sequences. Thus the foundations are set for a novel encoding based on L-systems for evolutionary approaches to both the Protein Structure Prediction and Inverse Folding Problems. © Springer-Verlag Berlin Heidelberg 2005.