Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion [new] ...enables precise engineering of diverse protein architectures and shape-encoded functions, including molecular swimmers.

Wally, our command-line genome alignment plotter, is now available as a client-only web app: no install, no upload, runs entirely in your browser: www.gear-genomics.com/wally/

Very happy to share my first preprint from my PhD 🎉 doi.org/10.64898/202... We develop an αHL-based framework to engineer and quantify selective diffusion across synthetic membranes using controlled nanopore chemistry. 1/7

Are you interested in working with a fresh team on cutting edge protein design? We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683... Please share!

Technical Assistant

jobs.dkfz.de

Are you interested in working with a fresh team on cutting edge protein design? We're hiring a Technical Assistant for our protein design team at DKFZ Heidelberg: jobs.dkfz.de/en/jobs/1683... Please share!

Technical Assistant

jobs.dkfz.de

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

Martin Pacesa@martinpacesa.bsky.social · 7mo ago

Huge congratulations @nboyd.bsky.social with Mosaic that absolutely killed in the competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 did also pretty well with the second highest hit rate in the competition! proteinbase.com/collections/...

Our latest cotranslational folding story is now published @cp-molcell.bsky.social. Really cool (I think) new ideas about how exactly the ribosome directs folding and assembly to make sure complicated proteins mature efficiently in cells. www.cell.com/molecular-ce...

The ribosome synchronizes folding and assembly to promote oligomeric protein biogenesis

Large oligomeric proteins constitute a major fraction of proteomes, but are difficult to refold in vitro, raising the question of how cells direct their biogenesis. Roeselová and Shivakumaraswamy et a...

cell.com

My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring! mirdita.org

Mirdita Lab - Laboratory for Computational Biology & Molecular Machine Learning

Mirdita Lab builds scalable bioinformatics methods.

mirdita.org

Second preprint of the year in which @sarahgersing.bsky.social from @rhp-lab.bsky.social mapped the effects of >7500 variants in glucokinase (GCK) on the interaction with the glucokinase regulatory protein so that we now have a 3D GCK scan (abundance, interaction, activity) doi.org/10.64898/202...

Rasmus Hartmann-Petersen@rhp-lab.bsky.social · 7mo ago

New preprint! Led by @sarahgersing.bsky.social we map how 7,500+ variants in glucokinase (GCK) affect binding to GKRP and disentangle this from stability. We now have activity, abundance, and interaction scores for 7,128 GCK variants - a resource for understanding phenotypes and glucose homeostasis.

This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell! This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍 [Maybe long thread ahead]

Toward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtii

Using the latest advances in instrumentation and computational workflows, Kelley et al. present a large-scale annotated cryo-electron tomography dataset of the model green alga, Chlamydomonas reinhard...

cell.com

Molecular Cell @cp-molcell.bsky.social · 7mo ago

The latest issue is now online www.cell.com/molecular-ce...

Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏

This was interesting and fun to do… seems Alphafold and the like have learnt what a Leucine zipper looks like… but not really.🤔 interesting that a fully synthetic leucine zipper that couldn’t possibly assemble looked pretty probable. 🧶🧬 doi.org/10.1002/pro....

Assessing the validity of leucine zipper constructs predicted by AlphaFold

AP-1 transcription factors are a network of cellular regulators that combine in different dimer pairs to control a range of pathways involved in differentiation, growth, and cell death. They dimerize...

doi.org

Xtals tree, 2026 edition. One structure for each user with finalized structure from current year. #crystallography #chemtree #chemchat #chemsky

Brand new preprint from my lab, showing that TnpB, the ancestor of Cas12, acts as a gene drive in plasmids! And it turns out in conjugative plasmids that it acts as a primitive anti-self defense system, providing a potential link between its transposon effect and becoming CRISPR!

Everyone's least favorite lab mate@kepatitis-c.bsky.social · 9mo ago

What is the best strategy to win any contest? Eliminate your opponents of course. Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight. www.biorxiv.org/content/10.1...

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

Tired of knowing what you are looking for in your tomograms? Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos) Code is on GitHub if you want to try it out

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 9mo ago

CryoSiam: self-supervised representation learning for automated analysis of cryo-electron tomograms https://www.biorxiv.org/content/10.1101/2025.11.11.687379v1

A few py2Dmol updates 🧬 py2dmol.solab.org Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

#1 lesson I give to protein designers for wet lab purposes : Please design with a Trp and/or multiple Tyr. Please do not design with 10 cysteines.

Has this idea of sampling neighbors from an inverse cubic distribution been used in protein structure GNNs at all since the idea was first presented in the Chroma paper ~3 years ago? I thought it was incredibly clever and expected it to catch on, but haven't seen it since

hey bsky! excited to share what i've been working on for a few years now. cryoJAX: A Cryo-EM Image Simulation Library In JAX www.biorxiv.org/content/10.1... cryoJAX is a modular framework for implementing forward models of cryo-EM image formation. these can be used to build powerful data analyses!

Global Analysis of Aggregation Determinants in Small Protein Domains https://www.biorxiv.org/content/10.1101/2025.11.11.687847v1

Are you an early-stage graduate student (2nd or 3rd year) or early-stage postdoc based in the US or Canada, working primarily in Drosophila? Would you like to help improve the experience of all trainees working in Drosophila research? If so, read on. (Please repost to reach a broad audience.)

#proteindesign #proteinbinder 100 designs ⬇️ 34 got through the screening (ipTM, PAE, RMSD) ⬇️ 4 ordered (gene synthesis + codon optimization) ⬇️ 3 expressed and soluble ⬇️ 1 interacts with its target !!!! Now the story begins !

a man with glasses and a mustache is wearing a white shirt and says yes .

ALT: a man with glasses and a mustache is wearing a white shirt and says yes .

media.tenor.com

Can an AI tool help us better understand the origins of cancer? Researchers from EMBL's Korbel Group have developed a new AI method – MAGIC – which, through a game of molecular laser tag, is shedding light on how chromosomal abnormalities form in cells. www.embl.org/news/science...

Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬 (feedback, suggestions, requests are welcome)

New review on experimental datasets that can be used to benchmark protein force fields. And if that doesn’t tickle your fancy, the data can also be used to benchmark machine learning models for biomolecular structure and dynamics.

@livecomsjournal.bsky.social · 9mo ago

In the latest @livecomsjournal.bsky.social perpetual review, Cavender et al overview NMR and crystallographic experimental datasets that can be used to benchmark protein force fields, including best practices for setup and analysis of simulations!: livecomsjournal.org/index.php/li... #compchem

Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography

Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...

biorxiv.org

**Job Alert** Exciting postdoc position available: theoretical and experimental cryo-EM studies of flexible biomolecules. Competitive salary, collaborative environment at NYSBC and Flatiron Institute. Please share!! and contact: pcossio@flatironinstitute.org

Opportunity in computational structural biology at ISTA (Vienna Austria) duration: 5 years with possibility of permanent contract #StructBiol #cryoEM #cryoET #chemsky 🧪 ista.ac.at/en/job/tenur...

Tenure-based Research Staff Scientist Position in Computational Structural Biology

ISTA (www.ista.ac.at) is seeking a highly skilled Staff Scientist in Computational Structural Biology to support and advance the Institute’s structural biology research through the development and imp...

ista.ac.at