CSConv2d: A 2-D Structural Convolution Neural Network with a Channel and Spatial Attention Mechanism for Protein-Ligand Binding Affinity Prediction

• Main Authors: Xun Wang, Dayan Liu, Jinfu Zhu, Alfonso Rodriguez-Paton, Tao Song
• Format: Article
• Language: English
• Published: MDPI AG 2021-04-01
• Series: Biomolecules
• Subjects: protein-ligand binding affinity; 2-D structural CNN; spatial attention mechanism
• Online Access: https://www.mdpi.com/2218-273X/11/5/643

The binding affinity of small molecules to receptor proteins is essential to drug discovery and drug repositioning. Chemical methods are often time-consuming and costly, and models for calculating the binding affinity are imperative. In this study, we propose a novel deep learning method, namely CSConv2d, for protein-ligand interactions’ prediction. The proposed method is improved by a DEEPScreen model using 2-D structural representations of compounds as input. Furthermore, a channel and spatial attention mechanism (CS) is added in feature abstractions. Data experiments conducted on ChEMBLv23 datasets show that CSConv2d performs better than the original DEEPScreen model in predicting protein-ligand binding affinity, as well as some state-of-the-art DTIs (drug-target interactions) prediction methods including DeepConv-DTI, CPI-Prediction, CPI-Prediction+CS, DeepGS and DeepGS+CS. In practice, the docking results of protein (PDB ID: 5ceo) and ligand (Chemical ID: 50D) and a series of kinase inhibitors are operated to verify the robustness.