PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture.

Abstract

The prediction of peptide secondary structures is fundamentally important to reveal the functional mechanisms of peptides with potential applications as therapeutic molecules. In this study, we propose a multi-view deep learning method named Peptide Secondary Structure Prediction based on Multi-View Information, Restriction and Transfer learning (PSSP-MVIRT) for peptide secondary structure prediction. To sufficiently exploit discriminative information, we introduce a multi-view fusion strategy to integrate different information from multiple perspectives, including sequential information, evolutionary information and hidden state information, respectively, and generate a unified feature space. Moreover, we construct a hybrid network architecture of Convolutional Neural Network and Bi-directional Gated Recurrent Unit to extract global and local features of peptides. Furthermore, we utilize transfer learning to effectively alleviate the lack of training samples (peptides with experimentally validated structures). Comparative results on independent tests demonstrate that our proposed method significantly outperforms state-of-the-art methods. In particular, our method exhibits better performance at the segment level, suggesting the strong ability of our model in capturing local discriminative information. The case study also shows that our PSSP-MVIRT achieves promising and robust performance in the prediction of new peptide secondary structures. Importantly, we establish a webserver to implement the proposed method, which is currently accessible via http://server.malab.cn/PSSP-MVIRT. We expect it can be a useful tool for the researchers of interest, facilitating the wide use of our method.