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© Oxford University Press

LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins

Francesco Vivarelli , Giuliano Giusti 1, Marco Villani , Renato Campanini , Piero Fariselli 2, Mario Compiani 3 and Rita Casadio 2,4

Department of Physics, University of Bologna I-40126 Bologna
1Corso di Laurea in Scienze dell'Informazione, University of Bologna I-47023 Cesena, (FO), Italy
2Laboratory of Biophysics, Department of Biology University of Bologna I-40126 Bologna
3Department of Chemical Sciences, University of Camerino I-62032 Camerino, Italy

4To whom reprint requests should be addressed

In this work we describe a parallel system consisting of feed-forward neural networks supervised by a local genetic algorithm. The system is implemented in a transputer architecture and is used to predict the secondary structures of globular proteins. This method allows a wide search in the parameter space of the neural networks and the determination of their optimal topology for the predictive task. Different neural network topologies are selected by the genetic algorithm on the basis of minimal values of mean square errors on the testing set. When the {alpha}-helix, ß-strand and random coil motifs of secondary structures are discriminated, the maximal efficiency obtained is 0.62, with correlation coefficients of 0.35, 0.31 and 0.37 respectively. This level of accuracy is similar to that previously attained by means of neural networks without hidden layers and using single protein sequences as input. The results validate the neural network topologies used for the prediction of protein secondary structures and highlight the relevance of the input information in determining the limit of their performance.

Received on September 20, 1994; revised on February 15, 1995; accepted on February 20, 1995

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[Abstract] [Full Text] [PDF]


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