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

New Title Alert: LASErMPNN- is an all-atom ligand-conditioned protein sequence design and sidechain packing model that accounts for the presence of small molecules, including hydrogens. Learn more here: buff.ly/cZcOmpC #SBGridSoftware #SBGrid #StructuralBiology

I’m looking to hire a research technician for my lab at Harvard & DFCI, who would primarily work in the wet lab expressing and characterizing designed proteins, starting this summer. A great role for a recent college grad looking for an immersive research experience before grad school.

Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition https://www.biorxiv.org/content/10.64898/2026.01.29.702630v1

Read the Save HHS open letter! www.savehhs.org/letter-we-wi...

The Cancer Signaling & Microenvironment Program at Fox Chase Cancer Center is looking for tenure track faculty (assist./assoc./full) in computational & experimental protein design. CV & 3-page research statement by Feb 15. More info here: www.linkedin.com/feed/update/... Questions: DM/Email me.

Happy New Year! We've got an exciting seminar to kick off 2026 Wednesday, January 21st at 7pm EST Room 181, Building 68 @mit.edu speaker: Erik Swanson and Mike Nichols "mBER: Controllable de novo antibody design with million-scale experimental screening" bpdmc.org

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens https://www.biorxiv.org/content/10.64898/2025.12.25.696505v1

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...

If you couldn't make it for @yehlincho.bsky.social's rockstar seminar last night, have no fear because you can check out the recording 👇 youtu.be/yCOlC_yj4kc

quick reminder to join us tonight for our final meeting of 2025 - it's going to be a great seminar by @yehlincho.bsky.social that you won't want to miss!

1/ Save the date! The 6th Protein Engineering Canada Conference will be held on June 22-24 in Ottawa, Canada. Abstract submission and registration are open! More information here: event.fourwaves.com/pec2026/pages

New preprint! Entropy drives molecular recognition, yet most structure-based drug design ignores it because it is difficult to measure. X-ray crystallography captures ensembles, not single structures. Can we extract thermodynamically meaningful entropy from them? www.biorxiv.org/content/10.1...

Don't fret if you weren't in the room this week when @ginaelnesr.bsky.social gave her stellar seminar because you can check out the recording 👇 youtu.be/I-utRMS84E8

@benf549.bsky.social made a nice little google colab notebook for running LASErMPNN for protein sequence design conditioned on ligands. Check it out! Feedback welcome. colab.research.google.com/github/poliz...

We can't wait until Wednesday, November 19th 2025 to arrive because we have @ginaelnesr.bsky.social from @possuhuanglab.bsky.social speaking at 7pm EST in Room 6055, Longwood Center, @danafarber.bsky.social "Learning millisecond protein dynamics from what is missing in NMR spectra" bpdmc.org

Last week to apply!

thanks everyone who packed the house tonight at @mit.edu for an incredible seminar by @grocklin.bsky.social!

quick reminder to come see @grocklin.bsky.social tonight at @mit.edu!

If you wonder why doesn't Harvard use its endowment: the answer, of course, is that we do. A major source of Harvard's annual budget is the endowment investment return. For anyone seriously interested in how university endowments work, an excellent wonky reference: www.nber.org/papers/w32506

now out in Protein Science! onlinelibrary.wiley.com/doi/10.1002/...

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.

quick reminder to join us at @danafarber.bsky.social tonight for a spectacular seminar by @marinkazitnik.bsky.social!

Our September seminar was delayed a couple weeks, but our speaker @marinkazitnik.bsky.social is well worth the wait. Join us this Wednesday, October 1st 2025 at 7pm EDT in Room 6055, Longwood Center, @danafarber.bsky.social "Empowering Biomedical Discovery with AI Scientists” bpdmc.org

Our latest article is now published online! In collaboration with @thompson-lab.bsky.social, Marc Garcia-Borràs, and @ferranfeixas.bsky.social. Distal Mutations in a Designed Retro-Aldolase Alter Loop Dynamics to Shift and Accelerate the Rate-Limiting Step pubs.acs.org/doi/full/10....

Interested in doing a postdoc at DFCI/Harvard on computationally designing and experimentally characterizing mini-protein binders for biomedical applications? Eric Fischer and I are looking for someone to work in our groups starting asap! Email me or my admin with a CV to apply!

Fun fact: #bindcraft evolved from a binder design tutorial originally developed for BPDMC! Come see @martinpacesa.bsky.social tonight at 7pm EDT in Room 181, Building 68, @mit.edu "BindCraft: one-shot design of functional protein binders" bpdmc.org

Happy to see this new T7 replicon based orthogonal replication system in E. coli. Congrats to the Diercks and Schultz lab teams at Scripps Research! www.science.org/doi/10.1126/...

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

The goal is catharsis and cackling. Boston-area: wanna play w/ soft, magnetic sculptures I made for neuro- & gender-spicy folks? Trans* to the front! No performance experience needed. $300 stipend (+ snacks!) for ~12 hrs collab. #bostonart #transart Apply by Aug 24: bit.ly/signal-sigil DM me Qs!

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

I still can’t believe that all NIH grants to my colleagues at Harvard and Harvard Medical School have been nullified. And that, as a nation, we’re somehow okay with this illegal, arbitrary, and petty act. Just think of the consequences: scientists, students, and patients will all suffer.

quick reminder to join us tonight at @harvardmed.bsky.social for a great talk by Colby Ford @colby.tuple.xyz

Learn about #AI tools in #protein #science, including design and engineering, at the EMBO Practical Course "AI for protein design" in Puerto Varas, Chile, 3–9 November 2025. Deadline: 1 August meetings.embo.org/event/25-ai-... #LifeSciences #research #training #ProteinStructure #EMBOevents 🧪

Now would be really good time to sign on in support of these courageous folks. We are at 5000 now, let's double that ASAP. www.standupforscience.net/epa-declarat...

#MorganLabatND is hiring a research technician!! We are looking for an aspiring biochemistry researcher that shares our community values, is curious about the world around them, and brings a unique perspective to our team. (1/2) jobs.smartrecruiters.com/UniversityOf...

Come learn about how to run the computational infrastructure that's powering the protein design revolution July 9th 2025 at 7pm EDT in TMEC250 @harvardmed.bsky.social "Model. Package. Deploy. Repeat: A DevOps Approach to Biomolecular Scalability" Colby Ford @colby.tuple.xyz bpdmc.org

We are looking to hire an Assistant/Associate Professor interested in creating an innovative (and exciting) program of research in chemical biology, medicinal chemistry, ML/AI, drug discovery - all in the context of cancer biology! careers.dana-farber.org/job/11813/as...

Franziska did a spectacularly successful PhD in my group and to a large extend set up the lab when we first started. I'm extremely happy for her (though not the least bit surprised) that she won these very important awards for her PhD. Watch this one, great things are certain to come.

How AlphaFold and related models predict protein-peptide complex structures https://www.biorxiv.org/content/10.1101/2025.06.18.660495v1

📢We are looking for a junior postdoc to join our lab. If you are interested on macrocyclic peptides and cancer immunotherapy, get in touch! ‼️spanish or/and catalan are required, since this position involves teaching duties 📩Deadline extended to June 30th

Don't fret if you missed Silvi Rouskin's brilliant and engaging talk on #RNA structure last night - you can check out the recording 👇 youtu.be/oS_Cb-YMymw

"We are speaking on behalf of hundreds of NIH staff who are standing up together to say: WE DISSENT. I am so scared about doing this but I am trying to be brave for my kids because it's only gonna get harder to speak up." Thank you to Dr. Jenna Norton and NIH scientists for your courage!

Funding freeze at Northwestern from Emma Mairson at grant-watch.us. Data from USAspending. Normally, ~$70 M per month. Now, bupkis. Northwestern is keeping research moving and must be spending ~$40 M per month. Clearly not sustainable for too long.

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

New paper from @nickpolizzi.bsky.social, Bill Degrado and Bobo Dang showing that de novo designed small molecule binding proteins can bind to the drug and clear it from the circulation in vivo. Read in Nature Biomedical Engineering! www.nature.com/articles/s41...

Protein isn't the only amazing macromolecule that folds into 3D shapes - come see Silvi Rouskin in Room 181, Building 68 at MIT on Wednesday, June 11th at 7pm EDT to learn more about #RNA structure design and modeling! "RNA Function, Design, and Modeling" bpdmc.org

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

New @biorxiv-biophys.bsky.social preprint from the #keedylab! 👀 www.biorxiv.org/content/10.1... How do related proteins perform distinct functions despite sharing a similar structure?...

from most recent Harvard lawsuit. sums it up pretty succinctly I think