{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/ss-gnn-a-simple-structured-graph-neural","title":"SS-GNN: A Simple-Structured Graph Neural Network for Affinity Prediction","arxiv_id":"2206.07015","date":"2022-05-25","proceeding":null,"authors":["Shuke Zhang","Yanzhao Jin","Tianmeng Liu","Qi Wang","Zhaohui Zhang","Shuliang Zhao","Bo Shan"],"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.","url_abs":"https://arxiv.org/abs/2206.07015v1","url_pdf":"https://arxiv.org/pdf/2206.07015v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"ss-gnn-a-simple-structured-graph-neural","repo_url":"https://github.com/xianyuco/ss-gnn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}}],"tasks":[{"task_slug":"graph-neural-network","task_name":"Graph Neural Network"},{"task_slug":"prediction","task_name":"Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2206.07015","atlas_url":"https://app.syntology.ai/?focus=2206.07015","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}