N. Evolving l-systems to capture protein structure native conformations.pdf

M. Keijzer et al. (Eds.): EuroGP 2005, LNCS 3447, pp X-XY, 2005, pp. 73 – 83, 2005. ? Springer-Verlag Berlin Heidelberg 2005 Evolving L-Systems to Capture Protein Structure Native Conformations Gabi Escuela1, Gabriela Ochoa2 and Natalio Krasnogor3 1,2 Department of Computer Science, Simon Bolivar University, Caracas, Venezuela gabiescuela@.ve, gabro@ldc.usb.ve 3 School of Computer Science and I.T., University of Nottingham Natalio.Krasnogor@nottingham.ac.uk Abstract. A protein is a linear chain of amino acids that folds into a unique func- tional 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 ap- proach 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. 1 Introduction The Protein Structure Prediction Problem (PSP) is among the most outstanding open problems in Biochemistry. A successful approach for efficient and accurate prediction would hasten a new era for biotechnology. A protein is as a linear sequence of units, called amino acids, that under certain physical conditions folds into a unique func- tional structure known as the native state or tertiary structure. This native state is the key to understanding a proteins’ functionality in a living organism as an enzyme, a storage, transport, mess