We seek to automate the generation of drug-like compounds conditioned to
specific protein pocket targets. Most current methods approximate the
protein-molecule distribution of a finite dataset and, therefore struggle to
generate molecules with significant binding improvement over the training
dataset. We instead frame the pocket-conditioned molecular generation task as
an RL problem and develop TacoGFN, a target conditional Generative Flow Network
model. Our method is explicitly encouraged to generate molecules with desired
properties as opposed to fitting on a pre-existing data distribution. To this
end, we develop transformer-based docking score prediction to speed up docking
score computation and propose TacoGFN to explore molecule space efficiently.
Furthermore, we incorporate several rounds of active learning where generated
samples are queried using a docking oracle to improve the docking score
prediction. This approach allows us to accurately explore as much of the
molecule landscape as we can afford computationally. Empirically, molecules
generated using TacoGFN and its variants significantly outperform all baseline
methods across every property (Docking score, QED, SA, Lipinski), while being
orders of magnitude faster.

我们致力于自动化生成与特定蛋白质口袋靶点相匹配的药物样化合物。我们采用强化学习方法，提出了一种目标条件生成流网络（TacoGFN）模型，通过该模型可以生成具有所需属性的分子。我们还开发了基于 Transformer 的对接评分预测方法，用于加速对接评分计算，并使用几轮主动学习来改善对接评分预测。实验证明，使用 TacoGFN 及其变种生成的分子在每个特性（对接评分，QED，SA，Lipinski）上显著优于所有基准方法，并且速度快了数个数量级。