Refined Contact Map Prediction of Peptides Based on GCN and ResNet

Jiawei Gu; Tianhao Zhang; Chunguo Wu; Yanchun Liang; Xiaohu Shi

doi:10.3389/fgene.2022.859626

Refined Contact Map Prediction of Peptides Based on GCN and ResNet

Front Genet. 2022 Apr 27:13:859626. doi: 10.3389/fgene.2022.859626. eCollection 2022.

Authors

Jiawei Gu¹, Tianhao Zhang¹, Chunguo Wu^{1

2}, Yanchun Liang^{1

2

3}, Xiaohu Shi^{1

2

3}

Affiliations

¹ College of Computer Science and Technology, University of Jilin, Changchun, China.
² Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, Changchun, China.
³ School of Computer Science, Zhuhai College of Science and Technology, Zhuhai, China.

Abstract

Predicting peptide inter-residue contact maps plays an important role in computational biology, which determines the topology of the peptide structure. However, due to the limited number of known homologous structures, there is still much room for inter-residue contact map prediction. Current models are not sufficient for capturing the high accuracy relationship between the residues, especially for those with a long-range distance. In this article, we developed a novel deep neural network framework to refine the rough contact map produced by the existing methods. The rough contact map is used to construct the residue graph that is processed by the graph convolutional neural network (GCN). GCN can better capture the global information and is therefore used to grasp the long-range contact relationship. The residual convolutional neural network is also applied in the framework for learning local information. We conducted the experiments on four different test datasets, and the inter-residue long-range contact map prediction accuracy demonstrates the effectiveness of our proposed method.

Keywords: deep learning; graph convolutional network; multiple sequence alignment; peptide inter-residue contact map prediction; residual convolutional neural network.