用生成式监督提升药物筛选的精准度,让模型更懂分子结合细节。
BindCLIP: A Unified Contrastive-Generative Representation Learning Framework for Virtual Screening
- 对比学习+生成建模联合训练,捕捉结合姿态级信息
- 在两个公开数据集上显著优于基线模型,尤其在分布外场景表现强
- 适合需要高精度排名的药物发现研究者使用
虚拟筛选旨在从大规模化学库中高效识别与目标蛋白口袋结合的活性配体。现有类似CLIP的模型(如DrugCLIP)通过将口袋和配体嵌入共享空间实现可扩展筛选,但分析表明其表征对细微结合相互作用不敏感,且可能依赖训练数据中的捷径关联,限制了基于真实结合兼容性的配体排序能力。为此,我们提出BindCLIP,一种统一的对比-生成表示学习框架。该框架联合使用CLIP式对比学习与口袋条件扩散模型生成结合姿态,使姿态级监督直接引导检索嵌入空间向交互相关特征靠拢。为减少捷径依赖,引入难负样本增强和配体-配体锚定正则化,防止表征坍缩。在两个公开基准上的实验显示,相比强基线有持续提升;在挑战性的分布外虚拟筛选任务中取得显著增益,并在FEP+基准上改善配体类似物排序。结果表明,整合生成式姿态监督与对比学习能获得更具交互感知能力的嵌入,提升真实筛选场景下的泛化性能,推动虚拟筛选向实际应用迈进。
原文摘要 · Abstract (English)
Virtual screening aims to efficiently identify active ligands from massive chemical libraries for a given target pocket. Recent CLIP-style models such as DrugCLIP enable scalable virtual screening by embedding pockets and ligands into a shared space. However, our analyses indicate that such representations can be insensitive to fine-grained binding interactions and may rely on shortcut correlations in training data, limiting their ability to rank ligands by true binding compatibility. To address these issues, we propose BindCLIP, a unified contrastive-generative representation learning framework for virtual screening. BindCLIP jointly trains pocket and ligand encoders using CLIP-style contrastive learning together with a pocket-conditioned diffusion objective for binding pose generation, so that pose-level supervision directly shapes the retrieval embedding space toward interaction-relevant features. To further mitigate shortcut reliance, we introduce hard-negative augmentation and a ligand-ligand anchoring regularizer that prevents representation collapse. Experiments on two public benchmarks demonstrate consistent improvements over strong baselines. BindCLIP achieves substantial gains on challenging out-of-distribution virtual screening and improves ligand-analogue ranking on the FEP+ benchmark. Together, these results indicate that integrating generative, pose-level supervision with contrastive learning yields more interaction-aware embeddings and improves generalization in realistic screening settings, bringing virtual screening closer to real-world applicability.
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