2023,
arXiv.
DOI:
10.48550/arXiv.2210.13695
arXiv ID:
2210.13695
Structure-based Drug Design with Equivariant Diffusion Models
Arne Schneuing, Yuanqi Du, Charles Harris, Arian Jamasb, Ilia Igashov, Weitao Du, Tom Blundell, Pietro Lió, Carla Gomes, Max Welling, Michael Bronstein, Bruno Correia
Abstract:
Structure-based drug design (SBDD) aims to design small-molecule ligands that bind with high affinity and specificity to pre-determined protein targets. In this paper, we formulate SBDD as a 3D-conditional generation problem and present DiffSBDD, an SE(3)-equivariant 3D-conditional diffusion model that generates novel ligands conditioned on protein pockets. Comprehensive in silico experiments demonstrate the efficiency and effectiveness of DiffSBDD in generating novel and diverse drug-like ligands with competitive docking scores. We further explore the flexibility of the diffusion framework for a broader range of tasks in drug design campaigns, such as off-the-shelf property optimization and partial molecular design with inpainting.
2023-07-31 22:52:30
尹志:
#paper doi: https://doi.org/10.48550/arXiv.2210.13695
Structure-based Drug Design with Equivariant Diffusion Models 又读了一遍这篇文献，用等变扩散模型进行结构化药物设计确实是一种有效的药物设计方式，越来越多的工作也在不断证明它的价值。这篇工作挺经典的（虽然貌似被iclr拒了），它基于蛋白质口袋利用se3等变扩散模型进行了分子生成。大量实验证明它生成药物分子的新颖性和多样性在效率和有效性上都很不错。文章还讨论了使用该方法对现有分子的优化，基于补全进行分子设计等问题，虽然在效果上还存在很多缺陷，但这些思路对于小分子药物设计及现有方法的改进都非常有价值。