Title:A Useful Tool for the Identification of DNA-binding Proteins Using Graph Convolutional Network
VOLUME: 18
Author(s):Dasheng Chen and Leyi Wei*
Affiliation:College of Intelligence and Computing, Tianjin University, Tianjin,, School of Software, Shandong University, Jinan
Keywords:DNA-binding proteins; graph convolutional network (GCN); protein sequence; sequence classification; deep learning;
k-mer spectrum.
Abstract:Background: Both DNAs and proteins are important components of living organisms. DNA-binding proteins are
a kind of helicase, which is a protein specifically responsible for binding to DNA single stranded regions. It plays a key role
in the function of various biomolecules. Although there are some prediction methods for the DNA-binding proteins sequences,
the use of graph neural networks in this research is still limited.
Objective: In this article, using graph neural networks, we developed a novel predictor GCN-DBP for protein classification
prediction.
Method: Each protein sequence is treated as a document in this study, and then document is segmented according to the
concept of k-mer. This research aims to use document word relationships and word co-occurrence as a corpus to construct a
text graph. Then, the predictor learns protein sequence information by two-layer graph convolutional networks.
Results: In order to compare the proposed method with other four existing methods, we have conducted more experiments.
Finally, we tested GCN-DBP on the independent data set PDB2272. Its accuracy reached 64.17% and MCC reached
28.32%.
Conclusion: The results show that the proposed method is superior to the other four methods and will be a useful tool for
protein classification.
