Gabriel Rocklin
@grocklin.bsky.social
Digests proteins. High-throughput protein biophysics and design, Northwestern University. www.rocklinlab.org
🚀 Excited to share our new work: Absolute Stability Predictor! 📊: forms.gle/4ZnXZSnTBvay... Built the MGnify Stability Dataset (1.8M+ measurements) and developed stability prediction models, together with @grocklin.bsky.social @KotaroTsuboyama, @sokrypton.org and teams.
We've actually been working on this very actively and have quite promising results on larger/higher stability proteins using an improved method. Looking for funding to buy some (a lot of) oligos... any pointers? It's within reach...
Thread coming later but I think people will like this!! 2 million stability measurements plus a predictive model for deltaG (not ddG)
bioRxiv Biophysics@biorxiv-biophys.bsky.social · 3mo agoAccurate protein stability prediction for small domains using mega-scale experiments https://www.biorxiv.org/content/10.64898/2026.05.19.726285v1
Accurate protein stability prediction for small domains using mega-scale experiments https://www.biorxiv.org/content/10.64898/2026.05.19.726285v1
Happy to share this in its published form! More than any project I've worked on, this was a huge team effort, so thank you so much to that team! Especially @ajrferrari.bsky.social www.nature.com/articles/s41...
Large-scale discovery, analysis and design of protein energy landscapes - Nature
An analysis of 5,778 domains 28–64 amino acids in length reveals hidden variation in conformational fluctuations, even between sequences sharing the same fold and global folding stability.
nature.com
Gabriel Rocklin@grocklin.bsky.social · last yr.Small proteins can be more complex than they look! We know proteins fluctuate between different conformations- but by how much? How does it vary from protein to protein? Can highly stable domains have low stability segments? @ajrferrari.bsky.social experimentally tested >5,000 domains to find out!
If you missed the preprint, now is a good time to read the journal version of @grocklin.bsky.social et al’s fantastic paper on multiplexed HDX measurements Large-scale discovery, analysis and design of protein energy landscapes doi.org/10.1038/s415...
bioRxiv Biophysics@biorxiv-biophys.bsky.social · last yr.Large-scale discovery, analysis, and design of protein energy landscapes https://www.biorxiv.org/content/10.1101/2025.03.20.644235v1
Another example demonstrating that the federal science and research ecosystem is being seriously damaged regardless of what’s ultimately appropriated
Laura Lopez@ohdearz.bsky.social · 4mo agoThis report came out today by minority staff of the House science committee on how three NASA missions were aborted due to NASA illegally following the FY26 president's budget request instead of congressionally approved budget. Very important reading. 🔭🧪 democrats-science.house.gov/staff-report...
NIGMS is signed onto the F31 NOFO. grants.nih.gov/grants/guide...
NOT-GM-26-002: Notice of NIGMS Participation in PA-25-422 "Ruth L. Kirschstein National Research Service Award (NRSA) Individual Predoctoral Fellowship (Parent F31)"
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Notice of NIGMS Participation in PA-25-422
grants.nih.gov
New lab preprint: if ML struggles with extrapolation, let's expand the diversity of training data with gene synth, DNA shuffling, and ML gen.... also lots of #FluorescentProteins #ProteinEngineering #MachineLearning #SyntheticBiology 1/n
bioRxiv Synthetic Biology@biorxiv-synthbio.bsky.social · 5mo agoHigh Diversity Gene Libraries Facilitate Machine Learning Guided Exploration of Fluorescent Protein Sequence Space https://www.biorxiv.org/content/10.64898/2026.03.01.706892v1
High Diversity Gene Libraries Facilitate Machine Learning Guided Exploration of Fluorescent Protein Sequence Space https://www.biorxiv.org/content/10.64898/2026.03.01.706892v1
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.
Here’s a preprint from the Keating Lab: www.biorxiv.org/content/10.6.... Foster Birnbaum and Amy E. Keating demonstrate that sequence design models, such as ProteinMPNN, are limited because they were trained only on native sequences.
biorxiv.org
The final Calvin and Hobbes, which appeared in papers 30 years ago today.
Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens [new] Mac1 co-folding eval: Pose prediction, conform. change, & hit ID post-training.
The most precious commodity you have is your attention. You don’t have to waste it on poor-faith debates or arguments with strangers if you don’t think they’ll be productive. You can prioritize the things that matter to you and make your life richer.
Excited to share our newest manuscript on antigen discovery and vaccine design for tuberculosis lead by Owen Leddy (everyone hiring new faculty in a few years, remember this name!) www.science.org/doi/10.1126/... #TBsky
Immunopeptidomics can inform the design of mRNA vaccines for the delivery of Mycobacterium tuberculosis MHC class II antigens
MHC class II immunopeptidomics in human phagocytes infected with Mycobacterium tuberculosis enables vaccine immunogen design and optimization.
science.org
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1
quick reminder to come see @grocklin.bsky.social tonight at @mit.edu!
Boston Protein Design and Modeling Club@bpdmc.org · 10mo agoJoin us in Room 181, Building 68 @mit.edu on October 22nd 2025 @ 7pm EDT to see @grocklin.bsky.social present a mind blowing amount of data and learn what becomes possible at this scale "Predicting protein folding stability and aggregation propensity using large-scale experiments" bpdmc.org
Join us in Room 181, Building 68 @mit.edu on October 22nd 2025 @ 7pm EDT to see @grocklin.bsky.social present a mind blowing amount of data and learn what becomes possible at this scale "Predicting protein folding stability and aggregation propensity using large-scale experiments" bpdmc.org
schedule
introduction and membership Boston Protein Design and Modeling Club (BPDMC) is a community of computational protein engineers and modelers from both academia and industry. While we are based in Boston...
bpdmc.org
Announcing such a major change to NSF GRFP this late in the cycle is incredibly cruel. 2nd yr students (mine included) have been working so hard on their proposals despite ongoing uncertainty. They are driven and passionate about being outstanding scientists and helping those coming up behind them.
Cecilia Payne-Gaposchkin ✨ figured out what stars are made of ✨ when she was just 25. 🔭🧪 Her PhD thesis basically established the Harvard astro department — at a time when Harvard didn't officially allow woman students. I wrote this little profile to mark the 100th anniversary of her thesis:
How a Harvard maverick forever changed our concept of the stars
At just 25, Cecilia Payne-Gaposchkin applied quantum physics to a treasure trove of astronomical observations to show that stars are mostly hydrogen and helium.
sciencenews.org
Sarah Tuttle@niais.bsky.social · 11mo agoWait a minute. Why aren't we celebrating the hundredth anniversary of Cecilia Payne-Gaposchkin's dissertation.
Vought and his “no more NIH money out the door” footnote is a power struggle. Between R’s getting antsy about hard votes and Senate signaling support for science funding, Vought had to signal his dominance in some way. Now is the real test: are R’s more afraid of Trump et al. or their constituents?
The NIH can’t award ANY grants to outside researchers under new WH restriction, reports @wsj.com. The pause came in the form of a footnote from OMB Director Vought, in a document that doles out federal funds to the NIH. Prelude to rescissions, especially after his comments over the weekend?
Trump Administration Puts New Chokehold on Billions in Health-Research Funding
The National Institutes of Health can’t award grants to outside researchers under a new White House restriction.
wsj.com
One might think, oh the fiscal year is only two months. But many of our grants are already delayed by weeks to months and we are on borrowed time as is. This is devastating and heralds darker times ahead.
Liz Essley Whyte@lizessleywhyte.bsky.social · last yr.NEW The White House is blocking the NIH from awarding new research grants for the rest of the fiscal year Chokes off billions in research funding Gift link www.wsj.com/politics/pol... with @nidhisubs.bsky.social
PO just confirmed that our 5th percentile R01 is not getting funded. Past NCI Payline at 4 percent. Cant believe it.
NCI's payline will be the 4th percentile. The Trump administration has effectively killed Cancer Research in the US www.cancer.gov/grants-train...
Funding Policy - Research Grants
NCI funding policy for research project grant (RPG) awards reflects the funding goals of the institute, NIH, and HHS.
cancer.gov
A motivating quote from @carolynbertozzi.bskyverified.social: “…You are discovering knowledge and gifting that to humanity for all of posterity. Once you learn something no one can take that away. It is not an object. It is an intellectual currency that will be shared throughout the generations…”
#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...
Research Technician
Company Description: The University of Notre Dame is more than a workplace; it is a vibrant, mission-driven community where every employee is valued and supported. Rooted in a tradition of excellence ...
jobs.smartrecruiters.com