Michael Jendrusch @mjendrusch.bsky.social · 22/09/2026Imagine my surprise seeing this today. If you were going to submit a short proposal for the 2027 CZS Nexus call, now's the time! Apparently there's only 37 slots left: www.carl-zeiss-stiftung.de/en/programme... 010
Reposted by Michael JendruschMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/09/2026BFVD v3 contains 5.8M viral protein structures, 16× more than v2; 75% high quality, filling a major gap in AFDB coverage. It fully covers 72.6% of reference proteomes and spans 72.7% of ICTV species. Great work by @eunbelivable.bsky.social et al. 📄 www.biorxiv.org/content/10.6... 🌐 bfvd.foldseek.com 18431
Reposted by Michael JendruschSergey Ovchinnikov @sokrypton.org · 15/08/2026getting close to recreating Jane Richardson's style 😎 412315
Reposted by Michael JendruschBryan Dickinson @chembiobryan.bsky.social · 06/08/20261/ Binder ≠ inhibitor. Most PPI inhibitor campaigns find a binder first, then hope it blocks the target protein-protein interaction. We built a system that skips the hoping and selects directly for disruption of a pre-formed PPI. Meet PANCS-Inhibitors. 🧵 www.biorxiv.org/content/10.6...biorxiv.orgPANCS-Inhibitors: A rapid method to directly select for protein-protein interaction inhibitorsAberrant protein-protein interactions (PPIs) drive myriad diseases. Inhibiting these PPIs often relies on discovering molecules that bind to one of the proteins and hoping that this binding inhibits t... 12211
Reposted by Michael JendruschAI x Bio Discovery @aixbiobot.bsky.social · 23/07/2026Programming 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. 051
Reposted by Michael JendruschTobias Rausch @trausch.bsky.social · 14/07/2026Wally, 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/ 261
Reposted by Michael JendruschElisabeth Bobkova @bobez.bsky.social · 01/06/2026Very 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. 1/7doi.org 123
Reposted by Michael JendruschMichael Jendrusch @mjendrusch.bsky.social · 02/03/2026Are 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!jobs.dkfz.deTechnical Assistant 01211
Michael Jendrusch @mjendrusch.bsky.social · 02/03/2026Are 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!jobs.dkfz.deTechnical Assistant 01211
Reposted by Michael JendruschMartin Pacesa @martinpacesa.bsky.social · 22/01/2026Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for. 22312
Reposted by Michael JendruschDavid Balchin @davidbalchin.bsky.social · 19/01/2026Our 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...cell.comThe ribosome synchronizes folding and assembly to promote oligomeric protein biogenesisLarge 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... 24423
Reposted by Michael JendruschMilot Mirdita @milot.bsky.social · 20/01/2026My 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.orgmirdita.orgMirdita Lab - Laboratory for Computational Biology & Molecular Machine LearningMirdita Lab builds scalable bioinformatics methods. 710756
Reposted by Michael JendruschKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/01/2026Second 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... 0236
Reposted by Michael JendruschRicardo D. Righetto @lifeonthewedge.bsky.social · 09/01/2026This 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]cell.comToward community-driven visual proteomics with large-scale cryo-electron tomography of Chlamydomonas reinhardtiiUsing 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... 39736
Reposted by Michael JendruschMartin Pacesa @martinpacesa.bsky.social · 26/12/2025Repeat after me: GENE 👏 EXPRESSION 👏 PROFILING 👏 DOES 👏 NOT 👏 A 👏 VIRTUAL 👏 CELL 👏 MAKE 👏 47916
Reposted by Michael JendruschKate Michie @kmichie.bsky.social · 23/12/2025This 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....doi.orgAssessing the validity of leucine zipper constructs predicted by AlphaFoldAP-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... 053
Reposted by Michael JendruschNikolay Tumanov @ntumanovxray.bsky.social · 20/12/2025Xtals tree, 2026 edition. One structure for each user with finalized structure from current year. #crystallography #chemtree #chemchat #chemsky 0153
Reposted by Michael JendruschMichael Baym @baym.lol · 20/11/2025Brand 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! 26328
Reposted by Michael JendruschGabriel Rocklin @grocklin.bsky.social · 19/11/2025New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains! 412241
Reposted by Michael JendruschRasmus Jensen @rasmusjensen.bsky.social · 19/11/2025Tired 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 05111
Reposted by Michael JendruschSergey Ovchinnikov @sokrypton.org · 19/11/2025A 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) 110331
Reposted by Michael JendruschKelvin Lau @klausenhauser on 🙅♂️🐘🪡 @klausenhauser.bsky.social · 18/11/2025#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. 2204
Reposted by Michael JendruschDiego del Alamo @delalamo.xyz · 16/11/2025Has 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 261
Reposted by Michael JendruschMichael O’Brien @m0bri3n.bsky.social · 14/11/2025hey 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!biorxiv.org 1132
Reposted by Michael JendruschbioRxiv Biophysics @biorxiv-biophys.bsky.social · 13/11/2025Global Analysis of Aggregation Determinants in Small Protein Domains www.biorxiv.org/content/10.1101/202… 01112
Reposted by Michael JendruschHarmit Singh Malik @harmitmalik.bsky.social · 12/11/2025Are 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.) 188179
Reposted by Michael JendruschAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 07/11/2025#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 !media.tenor.coma 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 . 2221
Reposted by Michael JendruschEMBL @embl.org · 29/10/2025Can 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... 0135
Reposted by Michael JendruschSergey Ovchinnikov @sokrypton.org · 29/10/2025Is 3D dragging you down? Wish you could instead use the 2D ColabFold representation for all your work? 🤓 Introducing: py2Dmol 🧬 (feedback, suggestions, requests are welcome) 1294
Reposted by Michael JendruschKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 28/10/2025New 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. 0215
Reposted by Michael JendruschRicardo D. Righetto @lifeonthewedge.bsky.social · 23/10/2025Our 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🍧biorxiv.orgIcecream: High-Fidelity Equivariant Cryo-Electron TomographyCryo-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... 45620
Reposted by Michael Jendruschpilarcossio.bsky.social @pilarcossio.bsky.social · 22/10/2025**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 01418
Reposted by Michael JendruschPeter Kenny @pwk2024.bsky.social · 16/10/2025Opportunity 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...ista.ac.atTenure-based Research Staff Scientist Position in Computational Structural BiologyISTA (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... 065
Reposted by Michael Jendruschjoe dobbs @joedobbs.bsky.social · 15/10/2025Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️ www.biorxiv.org/content/10.1... #teamtomo 811935
Reposted by Michael JendruschJosh Hardy @joshuamhardy.bsky.social · 28/09/2025I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5) doi.org/10.1101/2025.09.24.678028 #proteindesign 28731
Reposted by Michael JendruschJoe Grove @grovearmada.bsky.social · 26/09/2025🚨 New Web Resource Alert! 🚨 We're delighted to share Viro3D a database of >85000 viral protein structure predictions from >4400 human & animal viruses. 🔗 viro3d.cvr.gla.ac.uk 📄 www.embopress.org/doi/full/10.... @molsystbiol.org @cvrinfo.bsky.social @uofgmvls.bsky.social #Virology #AlphaFold 🧪 🦠viro3d.cvr.gla.ac.ukViro3D 14019
Reposted by Michael JendruschUlad Litvin @ulad-litvin.bsky.social · 26/09/2025Viro3D paper is out! We predicted 85,000 protein structures from human & animal viruses. 1/5 🧵 📑 Paper doi.org/10.1038/s443... 🔭 Explore virosphere viro3d.cvr.gla.ac.ukdoi.orgViro3D: a comprehensive database of virus protein structure predictions | Molecular Systems BiologyimageimageViro3D provides proteome-level, high confidence AI-protein structure predictions for >4,400 viruses, allowing mapping of form and function across the human and animal virosphere. Viro3D i... 15925
Michael Jendrusch @mjendrusch.bsky.social · 24/09/2025With this, the last bit of my PhD at @embl.org is finally out! We developed salad (sparse all-atom denoising), a family of blazing fast protein structure diffusion models. Paper: nature.com/articles/s42256-… Code: github.com/mjendrusch/salad Data: zenodo.org/records/14711580 1/🧵 1249
Reposted by Michael JendruschTJ McCorvie @allostericstate.bsky.social · 21/09/2025Part of something that we have been working on for a while-A 3.1 Å map of a flexibly tethered 38 kDa domain. Hopefully preprinted soon along with a few other structures. #CryoEM 5759
Reposted by Michael JendruschBen Engel @cellarchlab.com · 20/09/2025A molecular-resolution look into the near-native architecture of the spinach chloroplast🌱. This one was a long time in the oven, but we're happy to finally share our "version of record". What long-standing debates did we settle? Check back for a short thread🧵 on Monday. #TeamTomo #PlantScience 🧪🧶🧬🔬🌾 313446
Reposted by Michael JendruschMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 21/09/2025MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.comnature.comGPU-accelerated homology search with MMseqs2 - Nature MethodsGraphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio... 417463
Reposted by Michael JendruschHarry M. Williams @harrywilliams.bsky.social · 18/09/2025❄️ NEW PRE-PRINT ❄️ Happy to see our latest work online. Here we present a super simple solution to the preferred orientation problem in single particle cryo-EM: the use of ultrasonic excitation during vitrification! Details in the 🧵 below... #cryoEM #structuralbiology 12412
Reposted by Michael JendruschOli Clarke @olibclarke.bsky.social · 13/09/2025This one is a bit of a departure from the usual and definitely a work in progress! We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below. Read on for details... 1/x 2026782
Reposted by Michael Jendruschpaulschanda.bsky.social @paulschanda.bsky.social · 25/08/2025📢 New preprint: Aromatic Ring Flips Reveal Reshaping of Protein Dynamics in Crystals and Complexes. We addressed a long-standing question that people debated already in the 1970s - but it still remained open: Do proteins in crystals move as they do in solution? We used ring flips to find out. 1/n 24517
Reposted by Michael JendruschDaniel Fox @danielrfox.bsky.social · 02/09/2025Quite proud of this one. Our review on AI-designed de novo binders out now in Structure. We give a brief history, outline the current ecosystem, highlight some standout applications and discuss the need for regulatory discussions. 🤖🧪🔬sciencedirect.comCode to complex: AI-driven de novo binder designThe application of artificial intelligence to structural biology has transformed protein design from a conceptual challenge into a practical approach … 1195
Reposted by Michael JendruschMartin Pacesa @martinpacesa.bsky.social · 27/08/2025Exciting 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... 14305109
Reposted by Michael JendruschPossu Huang Lab @possuhuanglab.bsky.social · 19/08/2025We have a new collection of protein structure generative models which we call Protpardelle-1c. It builds on the original Protpardelle and is tailored for conditional generation: motif scaffolding and binder generation. 1215
Reposted by Michael JendruschMartin Pacesa @martinpacesa.bsky.social · 07/08/2025"Hey Bob, just dock the AF3 prediction into density and deposit" 3283
Reposted by Michael JendruschDavid Mills @millsgroupchem.bsky.social · 05/08/2025We are recruiting! Two 24 month postdoc positions are available with @m-l-baker.bsky.social and I, one mainly synthesis and the other measurements of lanthanide SMMs. Links below, deadline 19th Aug - please re-post: www.jobs.manchester.ac.uk/Job/JobDetai... www.jobs.manchester.ac.uk/Job/JobDetai...jobs.manchester.ac.ukResearch Associate in Synthetic Inorganic Chemistry:ManchesterAs an equal opportunities employer we welcome applicants from all sections of the community regardless of age, sex, gender (or gender identity), ethnicity, disability, sexual orientation and transgender status. All appointments are made on merit. 01213