Jeffrey J. Gray

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.

My latest manuscript is now on BioRxiv: Evaluation of De Novo Deep Learning Models on the Protein-Sugar Interactome. where we benchmark AF3 at protein-carbohydrate docking. This work was only possible with Dr. Lei Lu @takeshita-sho.bsky.social and @jeffreyjgray.bsky.social
doi.org/10.1101/2025...

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!

Would love to follow jazzway here instead of... Anywhere else

Our post-bac program will give you a year of research training after you finish undergraduate. Work on incredible biomolecular structure and design projects (e.g. antibody engineering, or deep learning algorithms), and have great mentoring and support in applying for grad schools and fellowships.

Winter RosettaCon: Early registration deadline extended to Jan 8
Good news! The early registration deadline for Winter RosettaCon has been extended to January 8.
Additionally, the travel award deadline has been extended to January 6.
Learn more: winterrosettacon.org

Join us to research protein design! After that Nobel Prize, the field is wide open for impactful applications in medicine, sustainability, and technology. It's an incredible summer.

We're excited to work with @omsf.io OpenADMET and @polarishub.io to bring you this blind predictive modeling community challenge!

If you're developing predictive models for drug discovery---potency or ADMET---here's your chance to test them prospectively on real discovery data from ASAP!

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

Deadline is Thurs Feb 1! Apply now for summer internships in computational biomolecular design.

(postbac apps due Feb 15)

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

Molecular ML Reading Group The Molecular ML Reading Group aims to explore foundational and recent applications of machine learning models to modeling molecular system.

Prepping for class this spring, this playlist of videos on diffusion models for proteins are great! Series is led by @maom.bsky.social and Nick Randolph of UNC.

www.youtube.com/playlist?lis...

Hey #NeurIPS2023 folks - interested in protein design / computational biology? Check out Rosetta Commons labs. We have undergrad summer internships, post-baccalaureate gap-year positions, and PhD programs and postdocs at universities around the globe.
www.rosettacommons.org/about

The Rosetta Commons REU (summer) and RaMP (postbac) applications are open! Apply to research in a molecular modeling and design laboratory. REU: rosettacommons.org/about/intern RaMP: rosettacommons.org/about/post-b... Application Help: docs.google.com/document/d/1... #Postbac #undergrad #compbio

Class photo of 27 participants from the 2023 Rosetta Commons summer REU/intern program.

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.

Late night experiment with @chrisfrank662.bsky.social :D
The backbone designability test. Start w/ backbone (diffusion, hallucination), put a sequence on it (proteinmpnn, esm-if), then the final test is to make sure it folds back to the original structure (alphafold, omegafold, esmfold) (1/3)

IgLM input-output model showing the infilling scheme.

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.

My department is hiring. apply.interfolio.com/136239

@rcsbpdb.bsky.social has joined Bluesky! Please follow them and post to them. Let's form a strong structural biology community on this site as the bird site continues to descend into...

Rosetta Commons Graduate Programs Rosetta Commons Graduate Programs Faculty,PI Website,Institution,Research areas,Program (PhD unless noted),Website,Needed background,Program Notes,2022 Deadline,Other Program Faculty of Interest,Prog...

Interested in graduate school in biomolecular structure prediction and design? Here's a list of graduate programs with faculty affiliated with the Rosetta Commons, a worldwide collaboration on software for biomolecular structure prediction and design, including AI/deep-learning approaches.

hope we can build another good protein science community here.

Thanks Roland, I'm in! So glad to be here.