Affiliations: Delhi College of Engineering, Bawana Road, New
Delhi-110042, India. E-mail: paras.chopra@bt.dce.edu; URL:
http://www.paraschopra.com | Novartis Institutes for BioMedical Research, Lead
Discovery Informatics, 250 Massachusetts Avenue, Cambridge/MA, USA. E-mail:
mail@andreasbender.de; URL: http://www.andreasbender.de/
Note: [] Corresponding author
Abstract: We demonstrate the first application of cellular automata to the
secondary structure predictions of proteins. Cellular automata use localized
interactions to simulate global phenomena, which resembles the protein folding
problem where individual residues interact locally to define the global protein
conformation. The protein's amino acid sequence was input into the cellular
automaton and rules for updating states were evolved using a genetic algorithm.
An optimized accuracy (Q3) for the RS126 and CB513 dataset of 58.21% and
56.51%, respectively, could be obtained. Thus, the current work demonstrates
the applicability of a rather simple algorithm on a problem as complex as
protein secondary structure prediction.
Keywords: Protein secondary structure prediction, protein folding, evolved cellular automata, genetic algorithms, secondary structure, protein fold, protein structure
