We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...
The results are finally in! 🏆💻🧬
I'm thrilled to announce that the manuscript for the Bits to Binders protein design competition is out on bioRxiv! Here's a summary of our findings, including some simple criteria that nearly *double* success rates when applied as a filter 🧵
Proteome-wide AlphaFold pool party N&V by @ksdrew.bsky.social link.springer.com/article/10.1... (I almost added a party GIF, almost :)
🔎 Exploring predicted complexes in the Complex Portal
Beyond curated entries, the portal also includes computationally predicted protein complexes.
Quick tour: tinyurl.com/2wph5wua
Includes:
🧬 hu.MAP 3.0
🎵 MuSIC
🧪 QSProteome
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/
New lab preprint - Common and rare variant studies for the same trait identify different genes and here Diederik Laman Trip developed a protein network AI enconding to investigate if traits studied by different approaches converge on the same molecular pathways
www.biorxiv.org/content/10.6...
Very sad to hear about the passing of Peer Bork, one of true giants of computational biology
www.embl.org/news/embl-an...
Video introduction to our new “Conformational Biasing” method for computational design of mutations that bias proteins towards desired conformational states
CB part starts at 14:55
Thanks to Peter Cavanagh and Andrew Xue – amazing graduate students who co-led this work
Congrats!
Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
RFpeptides made it to the cover of Nature Chemical Biology December issue!
Credit to Stephen Rettie for leading the work and making this very cool graphic!
Very happy to share our latest led by the relentless @shawnfayer.bsky.social! We developed multiplexed assays to measure variant effects across diverse genetic and cell contexts in stem cell and differentiated cells. 🧵 👇
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Congratulations to the newly minted Dr. Brittney Voigt! After defending a fantastic thesis spanning work in my lab and the @edwardmarcotte.bsky.social lab.
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Last week, the research of Rui Gao and lab was published by
@Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry.
science.org/doi/10.1126/...
The Gao lab at #UIC reports a breakthrough in volumetric fluorescence imaging, featured on the cover of Science Magazine!
Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
Congrats Qian www.science.org/doi/full/10....
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
Excited for you to join us!
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
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🧵
Also, I would like to thank the NSF and NIH for funding, and DOE Argonne, NSF ACCESS, and Indiana JetStream2 for computational resources.
There are lots of other results in the manuscript so please check it out. I definitely want to thank the team of Miles Woodcock-Girard, Erin Claussen, and Samantha Fischer who did the work.
