IP-GCN: A deep learning model for prediction of insulin using graph convolutional network for diabetes drug design

Abstract

Insulin is a kind of protein that regulates the blood sugar levels is significant to prevent complications associated with diabetes, such as cancer, neurodegenerative disorders, cardiovascular disease, and kidney damage. Insulin protein (IP) plays an active role in drug discovery, medicine, and therapeutic methods. Unlike experimental protocols, computational predictors are fast and can predict IP accurately. This work introduces a model, called IP-GCN for IP prediction. The patterns from IP are extracted by K-spaced position specific scoring matrix (KS-PSSM) and the model training is accomplished using powerful deep learning tool, called Graph Convolutional Network (GCN). Additionally, we implemented Pseudo Amino Acid Composition (PseAAC) and Dipeptide Composition (DPC) for feature encoding to assess the predictive performance of GCN. To evaluate the efficacy of our novel approach, we compare its performance with well-known deep/machine learning algorithms such as Convolutional Neural Network (CNN), Extremely Randomized Tree (ERT), and Support Vector Machine (SVM). Predictive results demonstrate that the proposed predictor (IP-GCN) secured the best performance on both training and testing datasets. The novel computational would be fruitful in diabetes drug discovery and contributes to research for therapeutic interventions in various Insulin protein associated diseases.