用曲率信息建模蛋白-配体结合动态,提升亲和力预测准确率。
Curvature-Informed Potential Energy Surface for Protein-Ligand Binding Affinity Prediction

- 基于势能面曲率构建动态特征,捕捉结合前后构象变化。
- 在多个基准数据集上优于现有方法,提升亲和力预测精度。
- 适合药物设计与分子动力学研究者,兼具可解释性。
精准预测蛋白-配体结合亲和力对结构导向药物发现至关重要。近年来,几何深度学习方法通过将蛋白-配体复合物表示为三维图,取得了良好效果。然而,多数方法仅依赖单一结合构象的静态相互作用几何,忽略了分子柔性及结合诱导的构象变化。为此,本文提出曲率感知势能面(CPES)图神经网络,引入物理启发的曲率表征以建模构象柔性。CPES首先从平衡构型处势能面的海森矩阵中提取曲率谱描述符,其特征值定义了势能面的局部主曲率;接着使用谱交叉注意力比较未结合的配体与蛋白和结合复合物,从而捕捉结合引起的构象动力学变化。同时,通过几何感知的消息传递、软聚类和双向交叉注意力,学习分层的蛋白-配体相互作用特征。最后,融合曲率驱动的动态表示与静态交互表示进行亲和力回归。在多个基准数据集上的广泛评估表明,CPES在预测性能上取得提升,并具备物理可解释性。
原文摘要 · Abstract (English)
Accurate prediction of protein-ligand binding affinity is essential for structure-based drug discovery. Recent geometric deep learning methods have achieved promising performance by representing protein-ligand complexes as three-dimensional graphs. However, most existing approaches mainly rely on static interaction geometry from a single bound conformation, while neglecting molecular flexibility and binding-induced conformational changes. To address this limitation, we propose a curvature-informed potential energy surface (CPES) graph neural network for protein-ligand binding affinity prediction, which incorporates physics-informed curvature representations to model conformational flexibility. CPES first derives curvature spectral descriptors from the Hessian of the potential energy surface evaluated at equilibrium configurations, whose eigenvalues define the local principal curvatures of the potential energy surface. It then uses spectral cross-attention to compare the unbound ligand and protein with the bound complex, thereby capturing binding-induced changes in conformational dynamics. In parallel, hierarchical protein-ligand interaction representations are learned from static structural features through geometry-aware message passing, soft clustering, and bidirectional cross-attention. Finally, CPES fuses the curvature-informed dynamic representations with static interaction representations for affinity regression. Extensive evaluations on multiple benchmark datasets demonstrate that CPES achieves improved predictive performance and offers physical interpretability.
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