Congratulations to @swcanner.bsky.social for the successful defense of his thesis, “The Protein Sugar Interactome”! Leveraging deep learning and AI, he created tools and uncovered putative structural interactions underlying intercellular communication. He will receive his diploma in December.

A comparison of DFMDock performance to Rosetta's top ranked structure. Read the preprint here: www.biorxiv.org/content/10.1...

By using an additional prediction head for an energy with its gradient matched to the score, we extract an energy function and compare it to Rosetta, an empirically tuned physically-inspired energy function. The learned energy sometimes recovers funnels with near-native minima, and sometimes not!

Excited to share our new preprint “Unified Sampling and Ranking for Protein Docking with DFMDock” by PhD candidate Lee-Shin Chu and Post-Doc Sudeep Sarma! We designed a diffusion docking model that samples rigid-body conformations by predicting forces and ranks poses using predicted energies.

Meet our new post-doc, Alejandra Montaño Romero! PhD in @cryoet.bsky.social’s lab (JHMI), she studied neurodevelopmental mutations in glutamate receptors via experimental & in silico work. Now she will improve deep learning for membrane proteins and design therapeutic antibodies targeting them!

Ice skating with the lab at the Johns Hopkins ice rink!

Superfun at #NeurIPS to see lab alumni Jeliazko Jeliazkov and @dakpinaroglu.bsky.social, here with current PhD students Michael Chungyoun and Fatima Hitawala.

As you are reflecting on your blessings this Thanksgiving, perhaps consider what wonderful scientific opportunities might be out there for you next summer! Join our programs for gap-year or summer research in protein design and AI.

Our infilling generative language model for antibodies, IgLM, is now published in Cell Systems!

This link is open-access for 50 days: authors.elsevier.com/a/1h-xe8YyDf...

Work of @richardshuai.bsky.social and @jeffruffolo.bsky.social.