Tootfinder

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly
Rohan V. Koodli, Alexander S. Powers, Ayush Pandit, Chiho Im, Ron O. Dror
https://arxiv.org/abs/2505.21833

A Graph Completion Method that Jointly Predicts Geometry and Topology Enables Effective Molecule Assembly
A common starting point for drug design is to find small chemical groups or "fragments" that form interactions with distinct subregions in a protein binding pocket. The subsequent challenge is to assemble these fragments into a molecule that has high affinity to the protein, by adding chemical bonds between atoms in different fragments. This "molecule assembly" task is particularly challenging because, initially, fragment positions are known only approximately. Prior methods for spatial graph c…