Kevin Drew

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…

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...

In remembrance of Peer Bork  | EMBL EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.

Very sad to hear about the passing of Peer Bork, one of true giants of computational biology

www.embl.org/news/embl-an...

YouTube video by Alice Ting Alice Ting Rosettacon keynote 2025

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

Computational design of conformation-biasing mutations to alter protein functions Conformational biasing (CB) is a rapid and streamlined computational method that uses contrastive scoring by inverse folding models to predict protein variants biased toward desired conformational sta...

Link to paper: www.science.org/doi/10.1126/...

Mapping proteins, one side chain at a time Roland Dunbrack Jr. will receive the ASBMB DeLano Award for Computational Biosciences at the ASBMB Annual Meeting, March 7–10, just outside of Washington, D.C.

This appeared today: www.asbmb.org/asbmb-today/...

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.

Proteome-wide in silico screening for human protein-protein interactions Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...

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.

Beyond Wolbachia—Can a small molecule control insect reproduction? Kaur et al. demonstrate reduced histone acetylation as a key mechanism underpinning Wolbachia’s paternal-effect embryonic lethality trait in Drosophila melanogaster. Recapitulation of this trait by in...

#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 🧬🧪

10 Rules for a Structural Bioinformatic Analysis The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

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...

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

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.

OFD1 disease mutations (pink) cluster at the OFD1(green)-FOPNL(orange) interface.

Finally, we utilize our network to build structural models of a ciliary protein complex linked to oral-facial-digital syndrome. We identified several human pathogenic mutations at the interface of OFD1 and FOPNL (CEP20), pointing to a mechanism of pathology.

The fraction of AlphaFold3 protein interaction models with high-confidence pDockQ pairs.

Encouraged by this, we prioritized ~2,500 high-confidence DirectContacts2 protein pairs and ran them through AF3. We see excellent enrichment of high quality models consistent with the AF2 models.

Comparison of enrichment for high-confidence pair interfaces out of the set of top confident pairs for DirectContacts2 and other networks. For each set, the fraction of high-confidence interfaces (pDockQ ≥ 0.5) out of their top predictions was calculated for increasing numbers of top predictions.

First, using a compendium of computed structural models for evaluation, we see our DirectContacts2 network outperforms other networks at prioritizing protein pairs for AlphaFold2 modeling.

Previous work by @bioinfo.se‬ and @pedrobeltrao.bsky.social‬, among others, prioritized pairs using protein interaction networks, including using our hu.MAP complex map.