Data-driven quantum chemical property prediction leveraging 3D conformations with Uni-Mol+

Shuqi Lu, Zhifeng Gao, Di He, Linfeng Zhang and Guolin Ke ()
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Shuqi Lu: DP Technology
Zhifeng Gao: DP Technology
Di He: Peking University
Linfeng Zhang: DP Technology
Guolin Ke: DP Technology

Nature Communications, 2024, vol. 15, issue 1, 1-11

Abstract: Abstract Quantum chemical (QC) property prediction is crucial for computational materials and drug design, but relies on expensive electronic structure calculations like density functional theory (DFT). Recent deep learning methods accelerate this process using 1D SMILES or 2D graphs as inputs but struggle to achieve high accuracy as most QC properties depend on refined 3D molecular equilibrium conformations. We introduce Uni-Mol+, a deep learning approach that leverages 3D conformations for accurate QC property prediction. Uni-Mol+ first generates a raw 3D conformation using RDKit then iteratively refines it towards DFT equilibrium conformation using neural networks, which is finally used to predict the QC properties. To effectively learn this conformation update process, we introduce a two-track Transformer model backbone and a novel training approach. Our benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets.

Date: 2024
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DOI: 10.1038/s41467-024-51321-w

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