ksdrew.bsky.social
Kevin Drew
@ksdrew.bsky.social
100 followers 110 following 30 posts
Assistant Professor at University of Illinois at Chicago (UIC) in Biological Sciences focused on macromolecular assemblies.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.

www.biorxiv.org/content/10.1...
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
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Reposted by Kevin Drew
kaurr.bsky.social
Rupinder Kaur, PhD @kaurr.bsky.social · 5d
#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...
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...
www.cell.com
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Reposted by Kevin Drew
bioinfo.se
Arne Elofsson @bioinfo.se · 9d
Congrats Qian www.science.org/doi/full/10....
www.science.org
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Reposted by Kevin Drew
computingcaitie.bsky.social
Caitie McCafferty @computingcaitie.bsky.social · 15d
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 🧬🧪
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Reposted by Kevin Drew
stephanieaw.bsky.social
Stephanie Wankowicz @stephanieaw.bsky.social · 27d
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...
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...
chemrxiv.org
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · 28d
Excited for you to join us!
kaurr.bsky.social
Rupinder Kaur, PhD @kaurr.bsky.social · 29d
Excited to share that I’ll be joining @uicbios.bsky.social as an Asst. Prof. in Jan 2026! My lab will explore the epi/genetic principles of host–microbe interactions, symbiosis, and vector biology. We’ll be hiring postdocs and techs—details and lab website coming soon!

bios.uic.edu/news-stories...
Meet the Faculty | Biological Sciences | University of Illinois Chicago
bios.uic.edu
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Reposted by Kevin Drew
kosonocky.bsky.social
Clay Kosonocky @kosonocky.bsky.social · Sep 2
🚨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!
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Reposted by Kevin Drew
martinpacesa.bsky.social
Martin Pacesa @martinpacesa.bsky.social · Aug 27
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...
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Reposted by Kevin Drew
yoakiyama.bsky.social
Yo Akiyama @yoakiyama.bsky.social · Aug 5
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🧵
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 ...
biorxiv.org
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
Also, I would like to thank the NSF and NIH for funding, and DOE Argonne, NSF ACCESS, and Indiana JetStream2 for computational resources.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
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.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
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.
OFD1 disease mutations (pink) cluster at the OFD1(green)-FOPNL(orange) interface.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
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.
The fraction of AlphaFold3 protein interaction models with high-confidence pDockQ pairs.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
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.
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.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
Previous work by @bioinfo.se‬ and @pedrobeltrao.bsky.social‬, among others, prioritized pairs using protein interaction networks, including using our hu.MAP complex map.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
We expect our network to be extremely valuable in applying computational structural modeling tools (e.g. AlphaFold, Boltz) to the human interactome. It is computationally infeasible to apply these algorithms to all ~200 million possible human pairwise interactions, so prioritization is key.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
We evaluated our network on a benchmark of known direct interactions from the PDB and see that it outperforms other networks including our previous attempt at solving this problem (DirectContacts doi.org/10.1371/jour...) and our hu.MAP co-complex networks!
Precision recall analysis shows the DirectContacts2 model (purple) outperforms the HuRI network (yellow), hu.MAP2.0 (green), hu.MAP3.0 (orange), and the original Direct Contacts model (blue). A random shuffling of pairs is shown in gray. Analysis is performed on a benchmark of leave-out set of direct (positive) and indirect (negative) protein interactions derived from the PDB.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
We integrated data from 25k mass spectrometry experiments (similar to our previous work, hu.MAP3.0, doi.org/10.1038/s443...), but this time trained on direct physical interactions from the PDB. We then applied our model to ~26M human protein pairs, giving a confidence score for each pair.
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
Determining whether two proteins have a direct physical interaction is an important (and difficult!) problem as protein complex assembly relies on physical interactions and protein interaction interfaces are the target of many therapeutics.
Image displays an illustrative, multi-subunit protein complex where some subunits directly interact (yellow and green subunits) while others indirectly interact through other subunits (magenta and green subunits).
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ksdrew.bsky.social
Kevin Drew @ksdrew.bsky.social · Jul 29
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.

www.biorxiv.org/content/10.1...
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
2 14 45
Reposted by Kevin Drew
konjikusicmia.bsky.social
Mia Konjikusic, PhD @konjikusicmia.bsky.social · Jul 19
‼️🚨Preprint alert! 🚨‼️
Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading!

www.biorxiv.org/content/10.1...
Primary cilia and BBS4 are required for postnatal pituitary development
Primary cilia orchestrate several signaling pathways, and their disruption results in pleiotropic disorders called ciliopathies. Bardet Beidl syndrome (BBS), one such ciliopathy, provides insights int...
www.biorxiv.org
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Reposted by Kevin Drew
wcratcliff.bsky.social
Will Ratcliff @wcratcliff.bsky.social · Jun 24
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬

www.science.org/doi/full/10....
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Reposted by Kevin Drew
franknoe.bsky.social
Frank Noe @franknoe.bsky.social · Jul 10
BioEmu now published in @science.org !!

What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
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Reposted by Kevin Drew
jbwallingford.bsky.social
John Wallingford @jbwallingford.bsky.social · Jul 1
Cilia Alert! So excited to finally have this paper on the CPLANE complex out in @natcomms.nature.com! We show that RSG1 is a human ciliopathy protein and links CPLANE to the transition zone. 1/n

www.nature.com/articles/s41...
The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture - Nature Communications
The CPLANE complex is essential for ciliogenesis, and mutations to all but one subunit have been associated with ciliopathies. Here they identify three familial mutations in the final subunit, RSG1, t...
www.nature.com
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Reposted by Kevin Drew
carolynbertozzi.bskyverified.social
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · Jun 30
Much appreciated support from biotech execs and investors 🙏

www.statnews.com/2025/06/27/b...
Proposed cuts could have ‘catastrophic effect,’ 110 biomedical, health sciences industry leaders tell Congress
Proposed cuts will have “a catastrophic effect on the advancement of biomedical and biotechnology capabilities in the United States,” more than 100 leaders of biomedical/health sciences companies tell...
www.statnews.com
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Reposted by Kevin Drew
umichmicroimmuno.bsky.social
U. Mich Micro-Immuno Dept @umichmicroimmuno.bsky.social · Jun 16
@bmoore-beth.bsky.social We are delighted to announce that Dr. Teresa O'Meara ‪was awarded the Henry Russel award at U-M. Our highest honor for an early-mid career faculty member for her outstanding research and teaching! @teresaomeara.bsky.social ‬ @umichmicroimmuno.bsky.social
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