A deep learning framework for improving protein interaction prediction using sequence properties

Abstract Motivation Almost all critical functions and processes in cells are sustained by the cellular networks of protein-protein interactions (PPIs), understanding these is therefore crucial in the investigation of biological systems. Despite all past efforts, we still lack high-quality PPI data for constructing the networks, which makes it challenging to study the functions of association of proteins. High-throughput experimental techniques have produced abundant data for systematically studying the cellular networks of a biological system and the development of computational method for PPI identification. Results We have developed a deep learning-based framework, named iPPI, for accurately predicting PPI on a proteome-wide scale depended only on sequence information. iPPI integrates the amino acid properties and compositions of protein sequence into a unified prediction framework using a hybrid deep neural network. Extensive tests demonstrated that iPPI can greatly outperform the state-of-the-art prediction methods in identifying PPIs. In addition, the iPPI prediction score can be related to the strength of protein-protein binding affinity and further showed the biological relevance of our deep learning framework to identify PPIs. Availability and Implementation iPPI is available as an open-source software and can be downloaded from https://github.com/model-lab/deeplearning.ppi Contact xiang-chen@zju.edu.cn