PIGNet2: a versatile deep learning-based protein-ligand interaction prediction model for binding affinity scoring and virtual screening

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Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep learning-based PLI prediction, the development of a versatile model capable of accurately scoring binding affinity and conducting efficient virtual screening remains a challenge. The main obstacle in achieving this lies in the scarcity of experimental structure-affinity data, which limits the generalization ability of existing models. Here, we propose a viable solution to address this challenge by introducing a novel data augmentation strategy combined with a physics-informed graph neural network. The model showed significant improvements in both scoring and screening, outperforming task-specific deep learning models in various tests including derivative benchmarks, and notably achieving results comparable to the state-of-the-art performance based on distance likelihood learning. This demonstrates the potential of this approach to drug discovery. PIGNet2, a versatile protein-ligand interaction prediction model that performs well in both molecule identification and optimization, demonstrates its potential in early-stage drug discovery.
Publisher
ROYAL SOC CHEMISTRY
Issue Date
2024-02
Language
English
Article Type
Article
Citation

DIGITAL DISCOVERY, v.3, no.2, pp.287 - 299

ISSN
2635-098X
DOI
10.1039/d3dd00149k
URI
http://hdl.handle.net/10203/319858
Appears in Collection
CH-Journal Papers(저널논문)
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