arXiv:2508.17555q-bio.BMcs.CE2025-08被引 7

用Docking引导的模型实现高效精准药物筛选,速度提升11.8倍。

Boltzina: Efficient and Accurate Virtual Screening via Docking-Guided Binding Prediction with Boltz-2

  • 基于Vina对接构象直接预测结合亲和力,跳过耗时结构预测步骤。
  • 在八组测试中比Vina和GNINA筛选效果更好,速度提升最高达11.8倍。
  • 支持多构象选择与两阶段筛选,适配不同精度与效率需求场景。

基于结构的药物发现中,传统分子对接虽快但预测精度有限。近期提出的Boltz-2模型在结合亲和力预测上精度极高,但每化合物每GPU需约20秒,难以用于数十万至数百万化合物的大规模筛选。本文提出Boltzina框架,利用Boltz-2的高精度优势,同时显著提升计算效率。通过省去Boltz-2中耗时的结构预测环节,直接从AutoDock Vina的对接构象预测亲和力,实现高精度与高速度兼顾。在MF-PCBA数据集的八个实验中,Boltzina虽略低于Boltz-2,但显著优于AutoDock Vina和GNINA。通过减少迭代次数和批量处理,速度最高提升11.8倍。研究还探索了多构象选择策略及两阶段筛选(Boltzina+Boltz-2)方法,可根据应用需求优化精度与效率。本工作首次将Boltz-2应用于实际规模筛选,提供兼具准确与高效的计算生物学流程。代码已开源:https://github.com/ohuelab/boltzina。

原文摘要 · Abstract (English)

In structure-based drug discovery, virtual screening using conventional molecular docking methods can be performed rapidly but suffers from limitations in prediction accuracy. Recently, Boltz-2 was proposed, achieving extremely high accuracy in binding affinity prediction, but requiring approximately 20 seconds per compound per GPU, making it difficult to apply to large-scale screening of hundreds of thousands to millions of compounds. This study proposes Boltzina, a novel framework that leverages Boltz-2's high accuracy while significantly improving computational efficiency. Boltzina achieves both accuracy and speed by omitting the rate-limiting structure prediction from Boltz-2's architecture and directly predicting affinity from AutoDock Vina docking poses. We evaluate on eight assays from the MF-PCBA dataset and show that while Boltzina performs below Boltz-2, it provides significantly higher screening performance compared to AutoDock Vina and GNINA. Additionally, Boltzina achieved up to 11.8$\times$ faster through reduced recycling iterations and batch processing. Furthermore, we investigated multi-pose selection strategies and two-stage screening combining Boltzina and Boltz-2, presenting optimization methods for accuracy and efficiency according to application requirements. This study represents the first attempt to apply Boltz-2's high-accuracy predictions to practical-scale screening, offering a pipeline that combines both accuracy and efficiency in computational biology. The Boltzina is available on github; https://github.com/ohuelab/boltzina.

虚拟筛选结合预测药物发现高效模型

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