Over the last few months, I have experimented with a return to TwiX. But it has weighed on me. It’s just not a community environment consistent with my values. Therefore, I am again suspending my use of TwiX. A couple reasons recently:

Enjoying a swing through New England. After a fun time at @bpdmc.org, Ethan Eschbach hosted me for a visit with @sandercbio.bsky.social and the @deboramarks.bsky.social lab. I was also thrilled to give a talk at the Thayer School of Engineering at Dartmouth hosted by T. Emme Burgin. What a fun week!

Thank you @sokrypton.org and @cdbahl.com for your hospitality and congrats to you for creating a warm scientific community at @bpdmc.org. I hope our discussion sparked new ideas about accelerating protein design and antibody engineering. Grateful for the chance to share my lab’s work!

Boston Protein Design and Modeling Club@bpdmc.org · 5mo ago

A huge thanks to everyone who packed the house at @mit.edu last night for a rockstar talk by @jeffreyjgray.bsky.social!

I'm so excited to speak at BPDMC this Wednesday evening! So many super protein scientists and modelers in Boston. I'm bringing some published and some unpublished work to share, hoping to spark some fun discussions.

Boston Protein Design and Modeling Club@bpdmc.org · 6mo ago

We've got Jeff Gray (graylab.jhu.edu) coming to present this month!! Wednesday, February 25th 2026, starting at 7pm EST in Room 181, Building 68, @MIT "Antibody language models vs. biology; protein docking denoising diffusion models vs. physics" bpdmc.org

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/

Undergraduates

Rosetta Commons Research Experience for Undergraduates (REU) AI for Biomolecular Structure Prediction and Design Interns in this geographically-distributed REU program participate in research using…

rosettacommons.org

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!

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! 🏒

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!

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.

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!

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.

Rosetta Commons@rosettacommons.bsky.social · 2y ago

The Rosetta Commons Research Experience for Undergraduates (REU) program accepts applications until February 1, 2025. Apply now and participate in research using the Rosetta Commons software. Learn more here: rosettacommons.org/education/reu/ #REU #RosettaCommons #Undergraduateprogram

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!

Polaris@polarishub.io · 2y ago

🦠 We’re excited to announce our first competition in partnership with @asapdiscovery.bsky.social and @omsf.io! Test your skills across three sub-challenges revolving around SARS-CoV-2 and MERS-CoV Mpro🧵 Full details: polarishub.io/competitions Blog: polarishub.io/blog/antivir...

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)

Jeffrey J. Gray@jeffreyjgray.bsky.social · 3y ago

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

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

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...

Molecular ML Reading Group

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

youtube.com

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

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)

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...

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.

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...

docs.google.com