Predicting secondary structures of membrane proteins with neural networks

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Abstract
Back-propagation, feed-forward neural networks are used to predict the secondary structures of membrane proteins whose structures are known to atomic resolution. These networks are trained on globular proteins and can predict globular protein structures having no homology to those of the training set with correlation coefficients (C) of 0.45, 0.32 and 0.43 for αa-helix, β-strand and random coil structures, respectively. When tested on membrane proteins, neural networks trained on globular proteins do, on average, correctly predict (Qi) 62%, 38% and 69% of the residues in the α-helix, β-strand and random coil structures. These scores rank higher than those obtained with the currently used statistical methods and are comparable to those obtained with the joint approaches tested so far on membrane proteins. The lower success score for β-strand as compared to the other structures suggests that the sample of β-strand patterns contained in the training set is less representative than those of a-helix and random coil. Our analysis, which includes the effects of the network parameters and of the structural composition of the training set on the prediction, shows that regular patterns of secondary structures can be successfully extrapolated from globular to membrane proteins.