Prediction of Protein-Protein Interactions Using Deep Learning Techniques

Abstract

Proteins are considered the primary actors in living organisms. Proteins mainly perform their functions by interacting with other proteins. Protein-protein interactions underpin various biological activities such as metabolic cycles, signal transduction, and immune response. PPI identification has been addressed by various experimental methods such as the yeast two-hybrid, mass spectrometry, and protein microarrays, to mention a few. However, due to the sheer number of proteins, experimental methods for finding interacting and non-interacting protein pairs are time-consuming and costly. Therefore a sequence-based framework called ProtInteract is developed to predict protein-protein interaction. ProtInteract comprises two components: first, a novel autoencoder architecture that encodes each protein's primary structure to a lower-dimensional vector while preserving its underlying sequential pattern by extracting uncorrelated attributes and more expressive descriptors. This leads to faster training of the second network, a deep convolutional neural network (CNN) that receives encoded proteins and predicts their interaction. Three different scenarios formulate the prediction task. In each scenario, the deep CNN predicts the class of a given encoded protein pair. Each class indicates different ranges of confidence scores corresponding to the probability of whether a predicted interaction occurs or not. The proposed framework features significantly low computational complexity and relatively fast response. The present study makes two significant contributions to the field of protein-protein interaction (PPI) prediction. Firstly, it addresses the computational challenges posed by the high dimensionality of protein datasets through the use of dimensionality reduction techniques, which extract highly informative sequence attributes. Secondly, the proposed framework, ProtInteract, utilises this information to identify the interaction characteristics of a protein based on its amino acid configuration. ProtInteract encodes the protein's primary structure into a lower-dimensional vector space, thereby reducing the computational complexity of PPI prediction. Our results provide evidence of the proposed framework's accuracy and efficiency in predicting protein-protein interactions.