arXiv:2507.11759cs.LG2025-07被引 1

用奖励信号训练模型,生成符合热力学分布的分子构象。

Torsional-GFN: a conditional conformation generator for small molecules

  • 基于条件GFlowNet,仅凭奖励函数学习分子扭转角采样。
  • 单个模型对多分子有效,且能零样本泛化到未见键长键角。
  • 适合药物构象采样,尤其适用于新分子快速生成。

生成稳定的分子构象在药物发现中至关重要,例如估算分子与靶标的结合亲和力。近年来,生成式机器学习方法成为比分子动力学更高效地从玻尔兹曼分布中采样构象的有力手段。本文提出Torsional-GFN,一种专门设计用于根据玻尔兹曼分布比例采样分子构象的条件生成流网络(GFlowNet),仅使用奖励函数作为训练信号。该模型以分子图及其局部结构(键长、键角)为条件,采样分子的扭转角。结果表明,Torsional-GFN可使用单一模型近似按玻尔兹曼分布采样多种分子的构象,并实现对来自分子动力学模拟的新未见键长与键角的零样本泛化。本工作为将该方法扩展至更大分子体系、实现对未见分子的零样本泛化,以及将局部结构生成纳入GFlowNet模型提供了有前景的方向。

原文摘要 · Abstract (English)

Generating stable molecular conformations is crucial in several drug discovery applications, such as estimating the binding affinity of a molecule to a target. Recently, generative machine learning methods have emerged as a promising, more efficient method than molecular dynamics for sampling of conformations from the Boltzmann distribution. In this paper, we introduce Torsional-GFN, a conditional GFlowNet specifically designed to sample conformations of molecules proportionally to their Boltzmann distribution, using only a reward function as training signal. Conditioned on a molecular graph and its local structure (bond lengths and angles), Torsional-GFN samples rotations of its torsion angles. Our results demonstrate that Torsional-GFN is able to sample conformations approximately proportional to the Boltzmann distribution for multiple molecules with a single model, and allows for zero-shot generalization to unseen bond lengths and angles coming from the MD simulations for such molecules. Our work presents a promising avenue for scaling the proposed approach to larger molecular systems, achieving zero-shot generalization to unseen molecules, and including the generation of the local structure into the GFlowNet model.

分子生成构象采样生成模型

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