通过梯度反演实现从头设计药物分子,提升结合亲和力。
MagicDock: Toward Docking-oriented De Novo Ligand Design via Gradient Inversion
- 采用梯度反演框架,利用结合预测生成反向梯度流引导分子生成。
- 在9个场景中平均优于当前最优方法27.1%(蛋白)和11.7%(分子)。
- 支持多种分子类型,适合新药研发人员快速生成高亲和力候选物。
从头药物分子设计旨在完全从零生成能有效与蛋白受体结合并具有强结合亲和力的分子候选物,对生物医学应用意义重大。然而,现有研究受限于伪从头设计、有限的对接建模和固定分子类型。为此,我们提出MagicDock,一个基于渐进式流程和可微表面建模的前瞻性框架。首先,将受体与配体的通用对接知识融入主模型,并通过结合预测实例化为反向梯度流,迭代引导分子生成。其次,在对接过程中强调可微表面建模,利用可学习的3D点云表示精确捕捉结合细节,确保生成分子具备直接可解释的空间指纹与对接有效性。第三,针对不同分子类型定制设计,并集成到统一的梯度反演框架中,支持灵活触发。此外,为每个组件提供严格的理论保证。在9个场景的大量实验表明,MagicDock在蛋白和分子类设计任务上分别平均优于当前最优基线27.1%和11.7%。
原文摘要 · Abstract (English)
De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.
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