用图神经网络提升隐式溶剂模型精度,实现高准确实用的自由能计算。
Extending machine learning model for implicit solvation to free energy calculations
- 引入图神经网络结合梯度匹配,解决传统方法能量偏移问题。
- 在约30万分子数据上训练,自由能预测精度媲美显式溶剂模拟。
- 适合需要快速精准自由能计算的药物设计场景。
隐式溶剂方法虽计算高效,但精度常不及显式溶剂模型,限制其在热力学精确计算中的应用。机器学习的发展为改进隐式溶剂势提供了新机遇。当前主流方法仅依赖力匹配,导致能量预测存在任意常数偏移,无法用于绝对自由能比较。本文提出基于图神经网络的隐式溶剂模型——Lambda Solvation Neural Network(LSNN),在力匹配基础上,额外匹配化学系综变量的导数,确保不同分子间溶剂化自由能可直接比较。模型在约30万个小分子数据集上训练,其自由能预测精度达到与显式溶剂全原子模拟相当的水平,同时实现显著计算加速,为药物发现等领域的应用奠定了基础。
原文摘要 · Abstract (English)
The implicit solvent approach offers a computationally efficient framework to model solvation effects in molecular simulations. However, its accuracy often falls short compared to explicit solvent models, limiting its use in precise thermodynamic calculations. Recent advancements in machine learning (ML) present an opportunity to overcome these limitations by leveraging neural networks to develop more precise implicit solvent potentials for diverse applications. A major drawback of current ML-based methods is their reliance on force-matching alone, which can lead to energy predictions that differ by an arbitrary constant and are therefore unsuitable for absolute free energy comparisons. Here, we introduce a novel methodology with a graph neural network (GNN)-based implicit solvent model, dubbed Lambda Solvation Neural Network (LSNN). In addition to force-matching, this network was trained to match the derivatives of alchemical variables, ensuring that solvation free energies can be meaningfully compared across chemical species. Trained on a dataset of approximately 300,000 small molecules, LSNN achieves free energy predictions with accuracy comparable to explicit-solvent alchemical simulations, while offering a computational speedup and establishing a foundational framework for future applications in drug discovery.
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