arXiv:2605.15564cs.LGcs.CE2026-05

用实验数据引导生成蛋白结构,33倍提速且精度更高

CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography

论文配图:CrystalBoltz: End-to-End Protein Structure Determination via Experiment-Guided Diffusion for X-Ray Crystallography
图 1 · 摘自论文原文
  • 将晶体学重构转为基于结构因子的贝叶斯推断
  • 在多个数据集上实现更低的坐标误差和更优的R因子
  • 适合需要快速高精度结构解析的研究者

基于公开蛋白结构数据库训练的生成模型,虽能提供有力的结构先验,但难以直接结合新晶体学实验的测量数据,限制了其在X射线晶体学结构确定中的应用。晶体学中,仅凭测得的结构因子振幅无法确定电子密度图或原子结构,因相位信息缺失,必须推断。因此结构确定仍是一个逆问题,需候选模型既符合结构合理性,又与衍射数据一致,常需大量人工精修。现有方法试图更直接地融入实验信息。本文提出CrystalBoltz,一种生成框架,将晶体学精修建模为对原子结构的贝叶斯推断,并直接处理结构因子振幅。该方法从无指导生成转向实验引导的后验采样,并进一步优化原子坐标与B因子。在多个蛋白质晶体学数据集上,CrystalBoltz在坐标均方根偏差(RMSD)和R因子方面优于最强基线,同时运行时间比现有实验引导精修方法减少33倍。

原文摘要 · Abstract (English)

Generative models trained on public databases of protein structures, most of which have been determined by X-ray crystallography, now provide powerful priors for structure prediction. However, they are not readily conditioned on the measurements from a new crystallographic experiment, limiting their use for X-ray structure determination. In crystallography, the measured structure-factor amplitudes do not by themselves determine an electron density map or atomic structure because the associated phases are unobserved and must be inferred. Structure determination therefore remains an inverse problem in which candidate models must be both structurally plausible and consistent with measured diffraction data, often requiring substantial manual refinement by human experts. Emerging methods aim to incorporate experimental information more directly into predictive and refinement workflows. We present CrystalBoltz, a generative framework that casts crystallographic refinement as Bayesian inference over atomic structures and operates directly on structure-factor amplitudes. CrystalBoltz moves from unguided generation with a pre-trained prior over protein structures to experiment-guided posterior sampling, followed by atomic coordinate and B-factor refinement. Across multiple protein crystallography datasets, CrystalBoltz attains lower coordinate RMSD and lower R-factors than the strongest baselines considered, while reducing runtime by a factor of 33 relative to existing experimentally guided refinement.

蛋白结构生成模型晶体学贝叶斯推断

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