SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction

• URL: http://arxiv.org/abs/2206.07015v1
• Date: Wed, 25 May 2022 04:47:13 GMT
• Title: SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction
• Authors: Shuke Zhang, Yanzhao Jin, Tianmeng Liu, Qi Wang, Zhaohui Zhang, Shuliang Zhao, Bo Shan
• Abstract summary: We propose a simple-structured graph neural network (GNN) model named SS-GNN to accurately predict drug-target binding affinity (DTBA) By constructing a single undirected graph based on a distance threshold to represent protein-ligand interactions, the scale of the graph data is greatly reduced. For a typical protein-ligand complex, affinity prediction takes only 0.2 ms.
• Score: 8.508602451200352
• License: http://creativecommons.org/licenses/by-nc-sa/4.0/
• Abstract: Efficient and effective drug-target binding affinity (DTBA) prediction is a challenging task due to the limited computational resources in practical applications and is a crucial basis for drug screening. Inspired by the good representation ability of graph neural networks (GNNs), we propose a simple-structured GNN model named SS-GNN to accurately predict DTBA. By constructing a single undirected graph based on a distance threshold to represent protein-ligand interactions, the scale of the graph data is greatly reduced. Moreover, ignoring covalent bonds in the protein further reduces the computational cost of the model. The GNN-MLP module takes the latent feature extraction of atoms and edges in the graph as two mutually independent processes. We also develop an edge-based atom-pair feature aggregation method to represent complex interactions and a graph pooling-based method to predict the binding affinity of the complex. We achieve state-of-the-art prediction performance using a simple model (with only 0.6M parameters) without introducing complicated geometric feature descriptions. SS-GNN achieves Pearson's Rp=0.853 on the PDBbind v2016 core set, outperforming state-of-the-art GNN-based methods by 5.2%. Moreover, the simplified model structure and concise data processing procedure improve the prediction efficiency of the model. For a typical protein-ligand complex, affinity prediction takes only 0.2 ms. All codes are freely accessible at https://github.com/xianyuco/SS-GNN.

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