@jeffreyjgray.bsky.social
Johns Hopkins Chemical & Biomolecular Engineering Professor, Co-Director of RosettaCommons, protein engineer, Baltimore resident, father of two. he/him
Final stretch to apply for undergraduate summer internships in the Rosetta Commons! Come design proteins, develop AI and physics-based methods to model biomolecules, and impact health, materials, and sustainability! Application deadline is Sunday Feb 1.
rosettacommons.org/education/reu/
For the new year, I’ll start posting again on X. I’m frustrated by its algorithm, uncivil discourse, and the owner's politics. But our work can also reach a much broader audience. Grateful to Jeremy Wang helping manage my social media. Excited to share more of our work!
21.01.2026 21:33 — 👍 1 🔁 0 💬 0 📌 0We updated our bioRxiv preprint last week to now include a succinct dimensional analysis of the major denoising diffusion equations. We summarize with a table that shows the meaning of each term in both AI and physics jargon.
23.12.2025 19:19 — 👍 1 🔁 0 💬 0 📌 0Our goal in this project was to explore methods whereby one might extract some ‘potential’ from AlphaFold3 to see why it is so much better than our traditional physics based approaches.
23.12.2025 19:18 — 👍 0 🔁 0 💬 0 📌 0
As someone trained in physics, this project really helped me learn the nuances of denoising diffusion models. The “time” variable acts as an alchemical transformation—e.g. RFDiffusion transforms between protein structure and an ideal gas.
Read the paper here!
www.biorxiv.org/content/10.1...
Meet our new JHU ChemBE PhD student, Matthew Adrian! He studied ChemE at UC Berkeley and developed MLDL methods for small molecule drug property prediction at Merck. His research will improve MLDL for protein binding prediction! Fun fact: Matt is the starting goalie for JHU Ice Hockey! 🏒
18.12.2025 18:16 — 👍 1 🔁 0 💬 0 📌 0
@britnie-carpentier.bsky.social presenting her Rosetta energy approximation network at European RosettaCon!
13.12.2025 15:15 — 👍 1 🔁 0 💬 1 📌 0
In these pictures, we are at the historic castle of Bled…lab members Britnie, Natalia, Fatima and friend Rebecca are the antibody and I’m an antigen! Thanks to @ajasjaljubetic.bsky.social and Dominic Gront for being amazing conference chairs and hosts!
13.12.2025 15:14 — 👍 2 🔁 1 💬 0 📌 0
Somewhat belated, but here’s our lab contingent at European Rosetta Con in Slovenia! As always, the welcoming @rosettacommons.bsky.social provided incredible scientific discussions, collaborations, and networking. With @britnie-carpentier.bsky.social, Natalia Rincon, and @fatimolecule.bsky.social!
13.12.2025 15:08 — 👍 5 🔁 1 💬 2 📌 0
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.
03.11.2025 14:24 — 👍 5 🔁 1 💬 0 📌 1
A comparison of DFMDock performance to Rosetta's top ranked structure. Read the preprint here: www.biorxiv.org/content/10.1...
08.10.2025 18:31 — 👍 0 🔁 0 💬 0 📌 0
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!
08.10.2025 18:28 — 👍 0 🔁 0 💬 0 📌 0
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.
08.10.2025 18:27 — 👍 7 🔁 4 💬 2 📌 0
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!
10.09.2025 17:52 — 👍 5 🔁 0 💬 0 📌 0Would love to follow jazzway here instead of... Anywhere else
04.05.2025 00:16 — 👍 1 🔁 0 💬 0 📌 0Our 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.
14.01.2025 16:15 — 👍 5 🔁 0 💬 0 📌 0Winter 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.
14.01.2025 16:12 — 👍 2 🔁 0 💬 0 📌 0We'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!
27.01.2024 15:14 — 👍 4 🔁 0 💬 0 📌 0Deadline 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.
18.12.2023 20:01 — 👍 5 🔁 0 💬 0 📌 0
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
20.11.2023 16:54 — 👍 5 🔁 3 💬 0 📌 1
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.
20.11.2023 16:53 — 👍 2 🔁 0 💬 1 📌 0
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
15.11.2023 18:49 — 👍 3 🔁 1 💬 0 📌 0
