Prediction of 8-state protein secondary structures by a novel deep learning architecture

Background: Protein secondary structure can be regarded as an information bridge that links the primary sequence and tertiary structure. Accurate 8-state secondary structure prediction can significantly give more precise and high resolution on structure-based properties analysis. Results: We present a novel deep learning architecture which exploits an integrative synergy of prediction by a convolutional neural network, residual network, and bidirectional recurrent neural network to improve the performance of protein secondary structure prediction. A local block comprised of convolutional filters and original input is designed for capturing local sequence features. The subsequent bidirectional recurrent neural network consisting of gated recurrent units can capture global context features. Furthermore, the residual network can improve the information flow between the hidden layers and the cascaded recurrent neural network. Our proposed deep network achieved 71.4% accuracy on the benchmark CB513 dataset for the 8-state prediction; and the ensemble learning by our model achieved 74% accuracy. Our model generalization capability is also evaluated on other three independent datasets CASH 0, CASH 1 and CASH 2 for both 8- and 3-state prediction. These prediction performances are superior to the state-of-the-art methods. Conclusion: Our experiment demonstrates that it is a valuable method for predicting protein secondary structure, and capturing local and global features concurrently is very useful in deep learning.