基于空间约束的生成模型,精准设计与靶蛋白匹配的药物分子。
SculptDrug : A Spatial Condition-Aware Bayesian Flow Model for Structure-based Drug Design
- 采用贝叶斯流网络框架,分步去噪提升分子空间构型精度。
- 引入边界感知模块,确保生成分子贴合蛋白质表面几何结构。
- 多层级编码器兼顾全局结构与局部相互作用,适合药物分子生成任务。
基于结构的药物设计(SBDD)利用三维蛋白质结构生成药物配体,但现有生成模型面临三大挑战:(1)边界条件约束难以融入,(2)多层次结构信息整合不足,(3)空间建模保真度低。为此,我们提出SculptDrug,一种基于贝叶斯流网络(BFNs)的空间条件感知生成模型。首先,SculptDrug采用基于BFN的框架,通过渐进式去噪策略提升空间建模保真度,逐步优化原子位置并增强局部相互作用,实现精确的空间对齐。其次,引入边界感知模块(Boundary Awareness Block),将蛋白质表面约束嵌入生成过程,确保生成配体在几何上与靶标蛋白兼容。第三,设计多层级编码器(Hierarchical Encoder),同时捕捉全局结构上下文与精细分子相互作用,保障整体一致性与准确的配体-蛋白构象。我们在CrossDocked数据集上评估SculptDrug,实验结果表明其优于现有先进基线模型,验证了空间条件感知建模的有效性。
原文摘要 · Abstract (English)
Structure-Based drug design (SBDD) has emerged as a popular approach in drug discovery, leveraging three-dimensional protein structures to generate drug ligands. However, existing generative models encounter several key challenges: (1) incorporating boundary condition constraints, (2) integrating hierarchical structural conditions, and (3) ensuring spatial modeling fidelity. To address these limitations, we propose SculptDrug, a spatial condition-aware generative model based on Bayesian flow networks (BFNs). First, SculptDrug follows a BFN-based framework and employs a progressive denoising strategy to ensure spatial modeling fidelity, iteratively refining atom positions while enhancing local interactions for precise spatial alignment. Second, we introduce a Boundary Awareness Block that incorporates protein surface constraints into the generative process to ensure that generated ligands are geometrically compatible with the target protein. Third, we design a Hierarchical Encoder that captures global structural context while preserving fine-grained molecular interactions, ensuring overall consistency and accurate ligand-protein conformations. We evaluate SculptDrug on the CrossDocked dataset, and experimental results demonstrate that SculptDrug outperforms state-of-the-art baselines, highlighting the effectiveness of spatial condition-aware modeling.
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