arXiv:2410.11226cs.LGq-bio.QM2024-10ICML被引 1

用多精度代理模型提升药物分子生成效果,显著改善结合自由能得分。

MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning

  • 融合多种成本-精度权衡的预测器,通过主动学习构建联合生成框架。
  • 在两种疾病相关蛋白上,平均结合自由能得分提升约50%。
  • 适合需要高精度药物分子设计的研究者,尤其关注计算效率与性能平衡。

当前药物发现中的生成模型主要依赖分子对接作为评估代理,但高对接评分的化合物在真实实验中活性并不稳定。更准确的活性预测方法如基于分子动力学的结合自由能计算虽更可靠,却因计算成本过高难以用于生成模型。为此,我们提出多精度潜在空间主动学习(MF-LAL)框架,整合多个不同成本-精度权衡的代理模型。通过主动学习为每个代理训练代理模型,并利用这些代理指导活性化合物生成。与以往分离训练代理与生成模型的方法不同,MF-LAL将生成模型与多精度代理模型统一于同一框架,实现更精准的活性预测和更高质量的分子样本。在两个疾病相关蛋白上的实验表明,MF-LAL生成的化合物相比其他单/多精度方法,平均结合自由能得分提升约50%。代码已公开于https://github.com/Rose-STL-Lab/MF-LAL。

原文摘要 · Abstract (English)

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show real-world experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches (~50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

药物生成主动学习多精度建模

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