Team science preprint, exploring the capabilities and limitations of Alphafold3 across different application areas, including protein-RNA, protein-lipid, ubiquitination,TCR and antibody recognition with @ninjani.bsky.social @labvanni.bsky.social @dgfeller.bsky.social www.biorxiv.org/content/10.6...

Capabilities, specificity gaps and training-data dependence of AlphaFold3 across diverse application areas

Structure prediction models have moved from single proteins to assemblies that include diverse biomolecules and their modifications. AlphaFold3 (AF3) and related models extended structural modelling v...

biorxiv.org

Happy to finally share that I will be starting my independent group at the @fmiscience.bsky.social in Feb 2027 in a vibrant new environment. We will use integrative in situ structural cell biology methods to investigate ciliary structure and dynamics in several model (and non-model 👀) systems!!

Welcome to our 2026 REU trainees! They spent the week at John Hopkins University completing an introductory bootcamp focused on machine learning and Rosetta software and tools. We can’t wait to see what they accomplish over the summer at their host labs throughout the US and Europe. zurl.co/LhlOI

🚀 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.

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!

1/ Thrilled to share our latest: an exciting collaboration across the @jshendure.bsky.social, @leastarita.bsky.social, @nobuhamazaki.bsky.social and @dschweppe.bsky.social labs! 🧵 below- #SystemsBiology #SCBEM #MultiOmics #Gastruloids www.nature.com/articles/s41...

The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology

Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.

nature.com

Excited to see @riddhiman.bsky.social's gastruloid multiomics paper out now at Nature Cell Bio! Riddhiman used proteomics, phosphoproteomics, and RNAseq to profile stem-cell-derived embryo models to identify protein, complex, and signaling regulators of development. www.nature.com/articles/s41...

The proteomic landscape and temporal dynamics of human and mouse gastruloid development - Nature Cell Biology

Garge et al. use experimentally matched mass spectrometry and RNA-sequencing to quantify proteins, phosphosites and transcripts across four key stages of human and mouse gastruloid development.

nature.com

I am excited to share our most recent work collaborating with @centriolelab.bsky.social and @stearnslab.bsky.social to look at the ciliary base of mammalian multiciliated cells w/ cryo-ET, XL/MS, and U-ExM www.biorxiv.org/content/10.6...

To better understand the ubiquitin-proteasome system, Suzanne Elsasser, Dan Finley, and the Human Proteostasis Consortium have systematically surveyed its components: www.biorxiv.org/content/10.6... I would encourage you to check out this valuable resource! @harvardcellbio.bsky.social

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...

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration

We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

evocellnet.com

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 :)

Proteome-wide AlphaFold pool party - Molecular Systems Biology

Molecular Systems Biology - An outstanding challenge in molecular biology is the production of a complete and accurate set of protein interactions for a given organism. Todor et al, introduce a...

link.springer.com

🔎 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/

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…

rosettacommons.org

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...

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.

embl.org

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

Alice Ting Rosettacon keynote 2025

YouTube video by Alice Ting

youtube.com

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

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...

science.org

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

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.

asbmb.org

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!

Nature Chemical Biology@natchembio.nature.com · 8mo ago

Our December issue is live! www.nature.com/nchembio/vol... The cover depicts a diffusion-based generative deep learning pipeline for de novo design of a macrocyclic peptide targeting the protein, myeloid cell leukemia 1

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. 🧵 👇

Shawn Fayer@shawnfayer.bsky.social · 9mo ago

The effects of genetic variants primarily occur in differentiated cells meaning we need to access these cell types to measure variant effects for most disease genes. We developed saturation genome editing in stem cells (iPSC-SGE) to enable phenotyping in diverse genetic and cell contexts at scale!

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

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...

biorxiv.org

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/...

Science Magazine@science.org · 10mo ago

A new method called VIPS enables organ-wide nanoscale reconstruction for quantitative mapping of connectivity and molecular landscape in intact tissue. Learn more this week in Science: https://scim.ag/4n4GKPm

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...

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...

cell.com

Congrats Qian www.science.org/doi/full/10....