GraphUnet-SS: A novel deep learning model for protein secondary structure prediction based on U-Net architecture

Prediction of the 3-D structure of a protein, which can be used to determine its function, is one of the most challenging problems in the bioinformatics field. Protein secondary structure prediction (PSSP) is a crucial step for protein 3-D structure prediction. Recent studies that focused on deep learning methods obtained significant improvements in PSSP. In this study, a novel deep learning model called GraphUnet-SS, which is based on the U-Net architecture and employs convolutional neural networks, graph convolutional networks, and bidirectional long short-term memories, is proposed. The feature set of the model consists of PSI-BLAST position-specific scoring matrices (PSSMs), HHBlits profiles, physico-chemical properties of amino acids, structural profiles for protein secondary structure, and a NoSeq label. A graph is generated using contact map prediction to represent the interactions between amino acids, which is used as input to graph convolutional network layers. The hyperparameters of GraphUnet-SS were optimized using the Bayesian optimization technique. Experimental results show that GraphUnet-SS outperforms the existing methods, and using all layers with depth four is the most suitable version. The source codes of the proposed method are available at https://github.com/ysngrmz/graph_unet_ss and the stand-alone version can be accessed at http://psp.agu.edu.tr/∼psp.