Book Chapter

Incorporating knowledge of secondary structures in a L-system-based encoding for protein folding



Ochoa G, Escuela G & Krasnogor N (2006) Incorporating knowledge of secondary structures in a L-system-based encoding for protein folding. In: Talbi E, Liardet P, Collet P, Lutton E & Schoenauer M (eds.) Artificial Evolution: 7th International Conference, Evolution Artificielle, EA 2005, Lille, France, October 26-28, 2005, Revised Selected Papers. Lecture Notes in Computer Science, 3871. Berlin Heidelberg: Springer, pp. 247-258.;

An encoding scheme for protein folding on lattice models, inspired by parametric L-systems, was proposed. The encoding incorporates problem domain knowledge in the form of predesigned production rules that capture commonly known secondary structures: α-helices and β-sheets. The ability of this encoding to capture protein native conformations was tested using an evolutionary algorithm as the inference procedure for discovering L-systems. Results confirmed the suitability of the proposed representation. It appears that the occurrence of motifs and sub-structures is an important component in protein folding, and these sub-structures may be captured by a grammar-based encoding. This line of research suggests novel and compact encoding schemes for protein folding that may have practical implications in solving meaningful problems in biotechnology such as structure prediction and protein folding.

Title of seriesLecture Notes in Computer Science
Number in series3871
Publication date31/12/2006
Publisher URL…0698_22?LI=true#
Place of publicationBerlin Heidelberg
ISSN of series0302-9743

People (1)


Professor Gabriela Ochoa

Professor Gabriela Ochoa

Professor, Computing Science