Protein Secondary Structure Prediction with Partially Recurrent Neural Networks

Abstract

Partially recurrent neural networks with different topologies are applied for secondary structure prediction of proteins. The state of some activations in the network is available after a pattern presentation via feedback connections as additional input during the processing of the next pattern in a sequence. A reference data set containing 91 proteins in the training set and 15 non-homologous proteins in the test set is used for training and testing a network with a modified, hierarchical Elman architecture. The network predicts the secondary structures α-helix, β-sheet, and “coil” for each amino acid. The percentage of correctly classified amino acids is 67.83% on the training set and 63.98% on the test set. The best performance of a three-layer feedforward network is 62.7% on the same test set. A cascaded network, where the outputs of the recurrent network are processed by a second net with 13 × 3 inputs, four hidden and three output units has a predictive performance of 64.49%. The best corresponding feedforward net has a performance of 64.3%.

Key Words:

• protein secondary structure prediction
• recurrent neural networks
• hierarchical architectures
• incremental training