A New Deep Neighbor Residual Network For Protein Secondary Structure Prediction

A protein secondary structure defines the local conformation of the protein's polypeptide backbone, which provides important information for protein 3D structure prediction and protein functions. In this study, a new deep neural network, the deep neighbor residual network (DeepNRN), is proposed for protein secondary structure predictions. The network takes three types of inputs, namely protein sequence features, profile features generated by PSI-BLAST, and profile features generated by HHBlits, and predicts the protein secondary structure in either one of eight states (Q8) or one of three states (Q3). The basic building block of the network, the neighbor residual unit, is designed with two types of short-cut connections that are more general and expressive than residual units in existing residual deep neural networks, yet can still be computed efficiently. In addition, the prediction result of DeepNRN can be refined by a Struct2Struct network to make the result more protein-like. Extensive experimental results on multiple widely used benchmark data sets show that the new DeepNRN-based method outperformed existing methods and obtained the best results across multiple data sets.