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Oli Clarke

@olibclarke.bsky.social
1.4K followers 968 following 552 posts

CryoEM, membrane proteins and whatnot

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Reposted by Oli Clarke
RCSB Protein Data Bank @rcsbpdb.bsky.social · 02/10/2026
Explore images that structural biologist Irina Bezsonova (UCONN Health) created for #inktober in PDB-101's #sciart gallery
pdb101.rcsb.org
PDB101: Irina Bezsonova Gallery
PDB-101: Training, Outreach, and Education portal of RCSB PDB
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Michelle Fry @myfry.bsky.social · 02/10/2026
1/ 🧵 Two classic mitochondrial pathways the TCA cycle and OXPHOS are taught as linked but distinct pathways. I’m happy to share our new work out in @cp-cell.bsky.social showing that in Acanthamoeba they're physically linked—with a TCA enzyme incorporated in ATP synthase. www.cell.com/cell/fulltex...
cell.com
Acanthamoeba ATP synthase structure reveals the TCA cycle is tethered to OXPHOS
Acanthamoeba castellanii, a pathogenic amoeba, belongs to an evolutionary branch distinctly removed from humans and fungi. Cryo-EM of the organism’s ATP synthase enzyme using raw mitochondrial lysates...
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Basil Greber @bjgreber.bsky.social · 01/10/2026
Those who had a careful look at the methods section of our work on the #cryoEM structure of the CDK11-cyclin L-SAP30BP complex will have noticed that we added a short peptide to our sample before freezing. If you wonder why...
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Oli Clarke @olibclarke.bsky.social · 30/09/2026
Added a couple of things to coot1-trimmings: * Option to set default model/map appearance to mimic Coot 0.9.x * Metal helper to semi-automatically make links for the current ion * Slider to interactively set map brightness (demos of brightness slider & metal helper in subsequent posts)
github.com
GitHub - olibclarke/coot1-trimmings: Customized keybindings and scripts for Coot 1.x
Customized keybindings and scripts for Coot 1.x. Contribute to olibclarke/coot1-trimmings development by creating an account on GitHub.
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Kiarash Jamali @kjamali.bsky.social · 29/09/2026
Please check out our cool new method, GuideFlip! Optimised for binders against disordered proteins
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Waggoner Lab @labwaggoner.bsky.social · 26/09/2026
Mammalian cells produce and store a sulfur compound for antioxidant protection @science.org www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...
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Oli Clarke @olibclarke.bsky.social · 26/09/2026
Sensational sunset in NYC tonight
Sunset with NY skylineLooking the other direction with extra rainbow
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cryoEM papers @cryoempapers.bsky.social · 26/09/2026
The CAHRA Challenge: A Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms pubmed.ncbi.nlm.nih.gov/42779743/ #cryoEM
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Rasmus Jensen @rasmusjensen.bsky.social · 25/09/2026
🎉 Out today in Cell: the paper I've been looking forward to sharing for a long time 🎉 We used cryo-ET to find a molecular machine nobody knew existed on the surface of a minimal bacterium, and worked out what it does. 🧵(1/7) #TeamTomo #cryoET
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Alex Noble @alexjamesnoble.bsky.social · 25/09/2026
We finally built what I've always wanted: A cryoEM papers database that is updated continually, searchable, and categorized! It's live right now at www.cryoarcana.com/cryoem-papers
CryoArcana CryoEM Papers Feed
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Vasilii Mikirtumov @vasiliimikirtumov.bsky.social · 24/09/2026
thrilled to share that my main phd project is finally out in @natcomms.nature.com we present high-resolution structures of RyR1 in native membranes across multiple functional states by both cryo-ET/StA #TeamTomo and SPA! paper: www.nature.com/articles/s41... and a thread below⬇️⬇️⬇️
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Laurel Oldach @laureloldach.bsky.social · 23/09/2026
Anthropic "CRISPR-like system" opinion: based on where the biochemical/wet-lab validation currently stands as reported in their not-a-preprint, this is a marketing document. The humans involved have made some v. cool mol-bio discoveries in the past, and evidently they expect this to also have ...
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Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
I'm excited to share our new preprint, where we show that fine-tuning gold nanoparticle conjugation to different Fab structural elements can produce powerful, rigidly coupled, labeling tools for in-situ cryo-ET. Take a look if you want to see an AuNP in an EM map!🔬🧠 www.biorxiv.org/content/10.6...
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Martin Pacesa @martinpacesa.bsky.social · 21/09/2026
ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 20/09/2026
Optimizing the connectivity of protein conformations to untangle ensemble refinement www.biorxiv.org/content/10.64898/20…
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Oli Clarke @olibclarke.bsky.social · 19/09/2026
looks pretty impressive
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 19/09/2026
BFVD 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
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Pedro Beltrao @pedrobeltrao.bsky.social · 18/09/2026
Anthropic has used Claude to optimise structure prediction and design code to improve speed and memory efficiency. 2-3X speed improvements on AF3, 5X on OF3, 5X on BindCraft low memory modes to model large assemblies. All released as open source www.anthropic.com/research/cla...
anthropic.com
How Claude is uplifting biomolecular modeling
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Milot Mirdita @milot.bsky.social · 16/09/2026
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim 🐍pip install colabfold[alphafold] CF2 Sneak Peak with AF3/Boltz/Protenix/ESMFold2… 🐍pip install "colabfold[alphafold3]@git+https://github.com/sokrypton/ColabFold@af3-preview"
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Alan Brown @alanbrownhms.bsky.social · 10/09/2026
Millions of beating cilia keep airways clean. At the base of each is the transition zone (TZ), a gate that controls which proteins enter and leave. In our paper out today in Science, we used cryo-FIB-ET to image the TZ inside human airway cells www.science.org/doi/10.1126/...
science.org
In situ structure of the human ciliary transition zone links linker defects to primary ciliary dyskinesia
The ciliary transition zone (TZ) regulates ciliary proteome composition, yet its molecular architecture, protein content, and contribution to motile ciliopathies remain poorly defined. We applied in situ cryo-electron tomography and subtomogram averaging ...
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Thelonevirologist @thelonevirologist.bsky.social · 07/09/2026
Bunsen burners’ reputation for sterilizing workplaces flames out www.nature.com/articles/d41...
nature.com
Bunsen burners’ reputation for sterilizing workplaces flames out
Study shows that the venerable device does not waft bacteria away from workbenches, as is often assumed.
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Magnus Bauer @kinasekid.bsky.social · 06/09/2026
AlphaFold Server’s ligand menu just got a lot bigger and I almost missed it! You can now add any ligand from the wwPDB Chemical Component Dictionary. Just enter its CCD code 🥳
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Max Kozlov @maxkozlov.bsky.social · 04/09/2026
Under pressure, the DOD just released the text of its secret 10-year agreement with the NIH. Here are the biggest revelations from the document 🧵
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Simon W Davis @woodforbrains.bsky.social · 03/09/2026
Ho-LEE fuck democrats-appropriations.house.gov/news/press-r...
democrats-appropriations.house.gov
Defense Officials Attempt to Raid NIH Funds to Cover Department of Defense Activities
House Appropriations Committee Ranking Member Rosa DeLauro (D-CT-03) has learned that officials at the Department of Defense (DoD) are working to divert billions of dollars from the National Institute...
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bioRxiv Biophysics @biorxiv-biophys.bsky.social · 28/08/2026
Structural basis for nutrient-activated channel opening in bacterial spore germination receptors www.biorxiv.org/content/10.64898/20…
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 26/08/2026
Foldseek-Interface enables fast search/clustering of the protein interface universe! We clustered 3.1M PDB dimers into 77,167 groups and found new interfaces keep appearing even as fold discovery plateaus. 🧵 📄 www.biorxiv.org/content/10.6... 🔎 search.foldseek.com/interface 🌐 interface.foldseek.com
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Structura Biotechnology @structurabio.bsky.social · 20/08/2026
🔬Malaria Invasion at Molecular Resolution: From Protein Inhibitors to Membrane Remodeling In a recent Cell publication, researchers at Columbia University resolved the endogenous structure of the malaria moving junction staple using #cryoEM. Read more in the #CryoSPARC Blog 👉 bit.ly/46aX6jl
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cryoEM papers @cryoempapers.bsky.social · 16/08/2026
cFAR and Relative Signal: Diagnosing Preferred Orientation in Single-Particle Cryo-EM www.biorxiv.org/content/10.64898/2026.08.11.744264v1 #cryoEM
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Sergey Ovchinnikov @sokrypton.org · 15/08/2026
getting close to recreating Jane Richardson's style 😎
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Structura Biotechnology @structurabio.bsky.social · 13/08/2026
🔄 Mixing Two Cryo-EM Datasets on Purpose: A Cryo-EM Heterogeneity Challenge What happens when you deliberately mix two #cryo-EM datasets containing different conformational states? Our latest #CryoSPARC blog distills the practical lessons from the accompanying FaNaC1 case study 👉 bit.ly/3ScIZa3
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Bryan Dickinson @chembiobryan.bsky.social · 06/08/2026
1/ 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.org
PANCS-Inhibitors: A rapid method to directly select for protein-protein interaction inhibitors
Aberrant 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...
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Tatta Bio @tattabio.bsky.social · 06/08/2026
SeqHub protein searches now show which regions of a predicted structure are tied to specific biological functions or evolutionary patterns, powered by @biohub.org's SAE features. 🧵
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Sven Lange @sven-m-lange.bsky.social · 05/08/2026
Some personal news: This September, I’ll be starting the Lange Lab at Weill Cornell Medicine as an Assistant Professor of Biochemistry and Biophysics! We’ll investigate how ubiquitin signals are decoded to control intracellular transport. sven-lange.xyz
sven-lange.xyz
Mechanisms of Ubiquitin-Mediated Transport
Lange Lab: Mechanisms of Ubiquitin-Mediated Transport
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Oli Clarke @olibclarke.bsky.social · 27/07/2026
I love @inaturalist.bsky.social - on my evening dog walk noticed that almost every hibiscus flower by the Harlem Meer had a sleepy bee inside - now I know that it is a hibiscus turret bee! 😊
Hibiscus flower with sleepy beeClose up of hibiscus beeCloser up of hibiscus bee
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Oli Clarke @olibclarke.bsky.social · 17/07/2026
@emdatabank.bsky.social EMPIAR entry for stomatin complex from @fravallese.bsky.social and myself released - I hope it will be useful for folks studying #cryoem compositional heterogeneity in pseudo/mixed symmetry systems, as classifying out AQP1 and UT-B was quite a challenge for us at least!
ebi.ac.uk
EMPIAR-13732 Stomatin encapsulates aquaporin-1 and urea transporter-B in the erythrocyte membrane
EMPIAR, the Electron Microscopy Public Image Archive centered at EMBL-EBI, is a public resource for raw electron microscopy images related to EMDB, contains micrographs, particle sets and tilt-ser...
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Kaitlyn Abe @kaitlynabe.bsky.social · 16/07/2026
1/5: Our latest preprint is out! We show that LEA proteins can diversify particle orientations in cryo-EM, helping to overcome preferred orientation at the air-water interface (AWI). www.biorxiv.org/cgi/content/... with @cijilim.bsky.social and Tim Grant #CryoEM #LEAproteins
biorxiv.org
Diversifying particle-orientation distributions in cryo-EM with LEA protein additives
Preferential orientation at the air-water interface (AWI) remains a persistent challenge in cryo-electron microscopy, often requiring extensive optimization or specialized grid preparation strategies....
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Bil Clemons @profbilc.bsky.social · 13/07/2026
I'm excited to announce a new preprint from the lab just posted to bioRxiv: “Retrograde trafficking inhibitors allosterically trap Get3 to block tail-anchored protein biogenesis.” www.biorxiv.org/content/10.6...
The structure of Human Get3 with the inhibitor Retro-2 bound in complex with Get4.
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Sternberg Lab @sternberglab.bsky.social · 09/07/2026
1/11 New preprint from the Sternberg lab in collaboration with the Fernández lab! We are excited to share our structure-function study of DRT10, a bacterial defense-associated reverse transcriptase that synthesizes long tandem-repeat DNA.🧵 Read the full story here: www.biorxiv.org/content/10.6...
biorxiv.org
Mechanism of tandem-repeat DNA synthesis by an antiviral reverse transcriptase
Defense-associated reverse transcriptases (DRTs) employ DNA synthesis to protect bacteria against phage infection[1][1],[2][2]. We previously showed that DRT10, a tripartite system comprising an RT, a...
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Neel Shah @nshahlab.bsky.social · 06/07/2026
Wow, this looks awesome and will be a great resource to anyone studying protein-protein interactions, SLiMs, and cell signaling! Excited to dig into this. Congrats to everyone involved!
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Oli Clarke @olibclarke.bsky.social · 04/07/2026
Pseudosymmetry in the wild 🙃🌻
Cluster of yellow Bird’s-foot trefoil flowers with almost six-fold symmetry.
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erzbergerlab.bsky.social @erzbergerlab.bsky.social · 02/07/2026
Membrane protein solubilization and structure determination using de novo–designed proteins | Science www.science.org/doi/10.1126/...
science.org
Membrane protein solubilization and structure determination using de novo–designed proteins
Developing therapies and vaccines against integral membrane proteins is hindered by their extensive hydrophobic surfaces, which complicate production and structural analysis. Here, we describe a gener...
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Oli Clarke @olibclarke.bsky.social · 02/07/2026
More weird RNAs! 🤯
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Carl Zimmer @carlzimmer.com · 01/07/2026
Meet SpudCell, a synthetic cell made from lifeless ingredients that feeds, grows, divides, and experiences selection. If it doesn't have all the hallmarks of life, it has a lot! Here's my story. Gift link: nyti.ms/4vCbTih
A series of images of a dividing synthetic cell
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Chi-Min Ho @cmholab.bsky.social · 30/06/2026
Incredibly proud of Messi Haile @mehsehret.bsky.social, a founding member of the Ho Lab, for her beautiful work uncovering the inner workings of a central piece of the malaria parasite invasion machinery: the malarial moving junction, out today in @cellpress.bsky.social! tinyurl.com/4p3md2eb 🦠❄️🔬
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De-Sheng Ker @kerds.bsky.social · 30/06/2026
We solved a high resolution structure of the nucleosome core particle directly from nuclear extract from a single T25 flask (3 mL culture). No affinity purification. No sucrose gradients. Just lysate on grids. Raw data available now for anyone who wants to reprocess. www.biorxiv.org/content/10.6...
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cryoEM papers @cryoempapers.bsky.social · 28/06/2026
Quinone-transporting filaments extend the respiratory chain of Gram positive bacteria www.biorxiv.org/content/10.64898/2026.06.26.734721v1 #cryoEM
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Andrew Plested @andrewplested.bsky.social · 27/06/2026
Wow. I love papers like this where you start off thinking “what? Sounds fishy” and then the data are so convincing and the paper so well written that is all so clear that you are blown away. Cells have a little aerial to allow them to move toward the anode!!! Galvanin! #PureScience #biophysics
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Silvia Ramundo @sramundo.bsky.social · 27/06/2026
Thanks, @olibclarke.bsky.social! Identifying this complex is good news for our job security as experimentalists... As of today, we still can’t predict the full assembly with AlphaFold. So here is an #open_challenge: if anyone can recover the whole complex computationally, I’d love to hear from them!
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Nature @nature.com · 25/06/2026
Nature research paper: Zero-shot design of drug-binding proteins via neural iterative selection−expansion go.nature.com/4eZ6yeW
go.nature.com
Zero-shot design of drug-binding proteins via neural iterative selection−expansion - Nature
 By pairing two neural networks in an iterative optimization algorithm, small-molecule binding proteins can be designed from scratch with high accuracy, affinity and success rates, showing promise for applications in drug delivery and sequestration.
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Oli Clarke @olibclarke.bsky.social · 24/06/2026
Amazing stuff, what a structure! Elegant work😍
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