TWIN模型实现水环境下的高精度分子模拟,速度比传统方法快100倍。
Transferable Implicit Solvent Machine Learning Potential for Drugs and Proteins Approaching Ab Initio Accuracy

- 用图神经网络从量子计算和实验数据训练隐式溶剂势能模型
- 在药物、肽和蛋白质上均达到接近量子力学精度的性能
- 适合需要快速高精度模拟的生物分子研究者使用
机器学习原子间势能(MLPs)革新了原子尺度建模,有望替代密度泛函理论(DFT)等传统方法。然而,现有MLP推理速度比经典力场慢多个数量级,难以满足微秒及以上时间尺度的生物分子模拟需求。隐式溶剂MLP虽可缓解此问题,但受限于粗粒化建模的数据挑战,以往方法依赖经验力场数据,限制了精度。本文提出可迁移的隐式水分子神经网络(TWIN),完全基于等变图神经网络,仅使用量子计算与实验标签进行训练。TWIN在药物分子、肽类和蛋白质上均表现出优异的可迁移性,在量子计算和实验晶体学、NMR基准测试中持续优于已有机器学习隐式溶剂或粗粒化模型。同时,其性能接近基于显式溶剂的DFT-MPL,且单步计算速度提升两个数量级,为水环境中生物分子的高效高精度建模铺平道路。
原文摘要 · Abstract (English)
Machine learning interatomic potentials (MLPs) have revolutionized atomistic modeling, offering the potential to replace traditional methods like Density Functional Theory (DFT). However, inference time of MLPs is orders of magnitude slower than that of classical force fields, hindering real-world applications for biomolecular systems that require timescales of microseconds and beyond. Implicit solvent MLPs can address this issue, but are faced with data challenges associated with coarse-grained modeling. Consequently, previous approaches relied on empirical force field data, thereby inherently limiting the MLP's accuracy. Here, we introduce the Transferable Water Implicit Network (TWIN), an implicit water MLP parametrized entirely by an Equivariant Graph Neural Network and trained solely on ab initio and experimental labels. We demonstrate TWIN's transferability across drug-like molecules, peptides, and proteins, achieving excellent results on ab initio and experimental crystallographic and NMR benchmarks, consistently outperforming previous machine-learning-based implicit solvent or coarse-grained models. Furthermore, TWIN closely matches DFT-based explicit solvent MLPs while providing a two-order-of-magnitude faster timestep evaluation, paving the way for efficient ab initio-level modeling of biomolecular systems in aqueous environments.
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