  In this work, we introduce AutoFragDiff, a fragment-based autoregressive
diffusion model for generating 3D molecular structures conditioned on target
protein structures. We employ geometric vector perceptrons to predict atom
types and spatial coordinates of new molecular fragments conditioned on
molecular scaffolds and protein pockets. Our approach improves the local
geometry of the resulting 3D molecules while maintaining high predicted binding
affinity to protein targets. The model can also perform scaffold extension from
user-provided starting molecular scaffold.
