DPB-NBFnet: Using neural Bellman-Ford networks to predict DNA-protein binding

• Main Authors: Jing Li (Author), Linlin Zhuo (Author), Xinze Lian (Author), Shiyao Pan (Author), Lei Xu (Author)
• Format: Book
• Published: Frontiers Media S.A., 2022-10-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.

Summary

DNA is a hereditary material that plays an essential role in micro-organisms and almost all other organisms. Meanwhile, proteins are a vital composition and principal undertaker of microbe movement. Therefore, studying the bindings between DNA and proteins is of high significance from the micro-biological point of view. In addition, the binding affinity prediction is beneficial for the study of drug design. However, existing experimental methods to identifying DNA-protein bindings are extremely expensive and time consuming. To solve this problem, many deep learning methods (including graph neural networks) have been developed to predict DNA-protein interactions. Our work possesses the same motivation and we put the latest Neural Bellman-Ford neural networks (NBFnets) into use to build pair representations of DNA and protein to predict the existence of DNA-protein binding (DPB). NBFnet is a graph neural network model that uses the Bellman-Ford algorithms to get pair representations and has been proven to have a state-of-the-art performance when used to solve the link prediction problem. After building the pair representations, we designed a feed-forward neural network structure and got a 2-D vector output as a predicted value of positive or negative samples. We conducted our experiments on 100 datasets from ENCODE datasets. Our experiments indicate that the performance of DPB-NBFnet is competitive when compared with the baseline models. We have also executed parameter tuning with different architectures to explore the structure of our framework.

Item Description

1663-9812
10.3389/fphar.2022.1018294