Prediction of Protein–ATP Binding Residues Based on Ensemble of Deep Convolutional Neural Networks and LightGBM Algorithm

Accurately identifying protein–ATP binding residues is important for protein function annotation and drug design. Previous studies have used classic machine-learning algorithms like support vector machine (SVM) and random forest to predict protein–ATP binding residues; however, as new machine-learning techniques are being developed, the prediction performance could be further improved. In this paper, an ensemble predictor that combines deep convolutional neural network and LightGBM with ensemble learning algorithm is proposed. Three subclassifiers have been developed, including a multi-incepResNet-based predictor, a multi-Xception-based predictor, and a LightGBM predictor. The final prediction result is the combination of outputs from three subclassifiers with optimized weight distribution. We examined the performance of our proposed predictor using two datasets: a classic ATP-binding benchmark dataset and a newly proposed ATP-binding dataset. Our predictor achieved area under the curve (AUC) values of 0.925 and 0.902 and Matthews Correlation Coefficient (MCC) values of 0.639 and 0.642, respectively, which are both better than other state-of-art prediction methods.