用神经网络快速找到分子构象变化的最低能量路径,效率提升数百倍。
Follow the MEP: Scalable Neural Representations for Minimum-Energy Path Discovery in Molecular Systems
- 将路径建模为隐式神经表示,通过可微力场进行端到端优化。
- 在标准GPU上用分钟级完成3500原子系统的路径发现,对比传统方法提速百倍。
- 适合研究大分子构象变化的生物物理与药物设计领域学者。
表征物理系统中的构象转变仍是根本性挑战,传统采样方法难以应对高维分子系统及状态间高能垒问题。这些罕见事件常代表重要生物学过程,但需数月连续模拟才能观测。最小能量路径(MEP)可揭示稳定态间的最可能过渡路径,适用于高摩擦、低温极限。本文提出一种新方法,将MEP发现转化为快速可扩展的神经优化问题。通过隐式神经表示路径并结合可微分子力场训练,无需昂贵采样即可发现过渡路径。方法基于奥恩萨格-马赫卢普作用量推导出简单损失函数,并采用新型可扩展架构AdaPath,成功应用于两个蛋白质系统,包括含3500多个原子的显式溶剂化BPTI体系。该方法在标准GPU上仅用几分钟即获得与毫秒级分子动力学模拟一致的构象变化路径,相较传统集群计算节省数周时间。
原文摘要 · Abstract (English)
Characterizing conformational transitions in physical systems remains a fundamental challenge, as traditional sampling methods struggle with the high-dimensional nature of molecular systems and high-energy barriers between stable states. These rare events often represent the most biologically significant processes, yet may require months of continuous simulation to observe. One way to understand the function and mechanics of such systems is through the minimum energy path (MEP), which represents the most probable transition pathway between stable states in the high-friction, low-temperature limit. We present a method that reformulates MEP discovery as a fast and scalable neural optimization problem. By representing paths as implicit neural representations and training with differentiable molecular force fields, our method discovers transition pathways without expensive sampling. Our approach scales to large biomolecular systems through a simple loss function derived from the path's likelihood via the Onsager-Machlup action and a scalable new architecture, AdaPath. We demonstrate this approach on two proteins, including an explicitly hydrated BPTI system with more than 3,500 atoms. Our method identifies a MEP that captures the same conformational change observed in a millisecond-scale molecular dynamics (MD) simulation in just minutes on a standard GPU, rather than weeks on a specialized cluster.
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