Design in Voxel Space Decode in SMILES Space: Plixer Generates Drug-Like Molecules for Protein Pockets
Jude Wells, Brooks Paige · bioRxiv (Cold Spring Harbor Laboratory) · 2025
Abstract We introduce Plixer, a two-stage generative model for de novo drug design that generates small-molecule ligand binders conditioned on an empty protein pocket. Plixer combines a conditional voxel inpainting network to generate 3D ligand hypotheses with an independently trained voxel-to-SMILES decoder that translates these voxel representations into valid chemical structures. By de-coupling the learning of spatial protein–ligand interactions from the learning of chemical grammar, our approach leverages large libraries of 3D ligand conformers to augment the limited data available for protein–ligand complexes. We show that this approach generates molecules with higher predicted binding affinity than recent methods.