Deep Geometry Handling and Fragment-wise Molecular 3D Graph Generation

Understand

Most earlier 3D structure-based molecular generation approaches follow an atom-wise paradigm, incrementally adding atoms to a partially built molecular fragment within protein pockets.

• These methods, while effective in designing tightly bound ligands, often overlook other essential properties such as synthesizability.
• The fragment-wise generation paradigm offers a promising solution.
• However, a common challenge across both atom-wise and fragment-wise methods lies in their limited ability to co-design plausible chemical and geometrical structures, resulting in distorted conformations.