Tufts University

End-to-end protein structure alignment from 3D coordinates, matching TM-align quality at LDDT 0.56 and beating Foldseek on SCOPe40 search.

Drug-target interaction model that compresses any compound into a 15-bit hierarchical code, so billion-compound libraries can be screened in seconds.

Autoregressive graph transformer generating molecules as node and edge token sequences, fine-tunable for goal-directed design and property prediction.

Metabolite annotation model embedding MS/MS spectra and molecular graphs in one contrastive space, ranking candidate structures by cosine similarity.

Macrocyclic peptide binder design against protein targets, cyclizing a diffusion backbone generator's positional encoding so it closes rings.