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In Silico Biology 7, 0007 (2006); ©2006, Bioinformation Systems e.V.  

Evolved cellular automata for protein secondary structure prediction imitate the determinants for folding observed in nature

Paras Chopra1* and Andreas Bender2

1 Delhi College of Engineering, Bawana Road, New Delhi-110042, India
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2 Novartis Institutes for BioMedical Research, Lead Discovery Informatics, 250 Massachusetts Avenue, Cambridge/MA, USA
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* Corresponding author

Edited by E. Wingender; received September 12, 2006; revised November 07 and December 10, 2006; accepted December 10, 2006; published December 11, 2006


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