Reposted by YC LinPhilippe Le Mercier, ViralZone @viralzone.bsky.social · 22/09/2026A clever new tool for building full icosahedral capsids from AlphaFold models — from the talented team behind ViperDB. FoldaVirus, a knowledge-based icosahedral capsid prediction tool using AlphaFold www.pnas.org/doi/10.1073/... 0118
Reposted by YC LinAlexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 21/09/2026Nice talk, really perfect for teaching Everything you've always wanted to know about #AlphaFold, iPTM, PAE, pLDDT, and ipSAE but were afraid to ask 1275
Reposted by YC LinMartin Pacesa @martinpacesa.bsky.social · 21/09/2026ʙɪɴᴅᴄʀᴀꜰᴛ2 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... 4292142
Reposted by YC LinMartin 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 YC LinMilot Mirdita @milot.bsky.social · 16/09/2026ColabFold 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" 29736
Reposted by YC LinKumaran Ramamurthi @ramamurthilab.bsky.social · 15/09/2026How do proteins localize in bacteria? Usually by binding to a prelocalized protein-but how does that protein localize? @vanipande.bsky.social found a #Bacillus subtilis protein that localizes via a lipid cue,undecaprenyl phosphate,that guides it to sites of PG synthesis www.pnas.org/doi/10.1073/...pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans... 14214
Reposted by YC LinSergey Ovchinnikov @sokrypton.org · 14/09/2026Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr) 727698
Reposted by YC LinMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/ 215759
Reposted by YC LinProtein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 10/09/2026Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB 172
Reposted by YC LinMagnus Bauer @kinasekid.bsky.social · 06/09/2026AlphaFold 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 🥳 16028
Reposted by YC Lincorrylab.bsky.social @corrylab.bsky.social · 01/09/2026Excited to share work by @yemilywang.bsky.social & Zhouyu Zhang, in a collab with PKU: Martini 3 CG sims overestimate lipid scrambling, predict it in proteins that don't scramble, and give anomalous binding, from low headgroup polarity. But small parameter refinements fix it. tinyurl.com/m3scramble 0103
Reposted by YC LinMartin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/08/2026Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w... 117841
Reposted by YC LinRobert Arkowitz @robertarkowitz.bsky.social · 18/08/2026www.pnas.org/post/journal...pnas.orgProbes show lipids are far more selective for proteins than once thoughtLipids, according to recent findings, are not just diffusing randomly around the lipid bilayer (shown here), but actually have specific proteins they like to pair with. Image credit: Science Source/K... 0225
Reposted by YC Linhenrietteautzen.bsky.social @henrietteautzen.bsky.social · 12/08/2026Happy to see our NHE6 story published today in @natcomms.nature.com! Led by @lukasfeilen.bsky.social we reveal the #cryoEM structure, ion selectivity and regulation of the endosomal Na+/H+ exchanger NHE6, providing a framework for understanding Christianson syndrome. www.nature.com/articles/s41... 23413
Reposted by YC LinStephanie Wankowicz @stephanieaw.bsky.social · 11/08/2026Most PDB structures report one set of coordinates. But the experimental data behind them, in both X-ray crystallography and cryo-EM, is produced by an ensemble of structures. How to extract this ensemble data at scale has been a quest in structural biology for 40+ years. 25115
Reposted by YC LinNature Portfolio @natureportfolio.nature.com · 06/08/2026Review mills — researchers who write fake referee reports with coercive citation requests — are setting off a war in academic publishing. Nature reports on what happens to those caught in the middle. #Academicsky 🧪go.nature.com‘A waste of time for all of us’: caught in the crossfire of the peer-review warsReview mills — researchers who write fake referee reports with coercive citation requests — are setting off a war in academic publishing. What happens to those caught in the middle? 0167
Reposted by YC LinRan Blekhman @blekhman.bsky.social · 27/06/2026I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...open.substack.comMy Peer Review of The 1%I wanted to like QED's new 1% ranking. I don't. 1720888
Reposted by YC LinOded Rechavi @odedrechavi.bsky.social · 23/06/2026Time from submission to acceptance: 3 UK Prime Ministers. 712613
Reposted by YC LinReichow Lab @reichowlab.bsky.social · 01/06/2026Dual-channel Cx46/50 gap junction assemblies in a shared lipid-nanodisc = lipid-mediated packing and a lipid site near the NT gating region that is absent from single channels. Plus a 1.8 Å open-state single-channel benchmark! #cryo-EM 🍩’s #NIH-funded-research www.biorxiv.org/content/10.6... 44813
Reposted by YC LinBrady Johnston @bradyajohnston.bsky.social · 28/05/2026Some very cool simulations, look at those little guys climb that ladder! #MolecularNodes 09725
Reposted by YC LinKate Michie @kmichie.bsky.social · 09/04/2026Our paper is out today! See this news article on it. Asgard archea have some cool proteins. If you are interested in protein evolution it’s a really exciting space. I’m lucky to be a structural biologist in the age of DL🧬🧶 @brendanburns999.bsky.social @iduggin.bsky.social @debnathghosal.bsky.socialphys.orgFrom Asgard to Earth: Tiny tubes may reveal the moment complex life beganStromatolites—and their close relatives, microbial mats—could be mistaken for what seems like a bunch of old dark rocks. But instead, they are dense, layered communities of microbes. Long before compl... 15118
Reposted by YC LinNature @nature.com · 17/03/2026AlphaFold database now includes 1.7 million 'homodimers' - comprising two interacting strands of the same molecule go.nature.com/4cSmbnTgo.nature.comAlphaFold hits ‘next level’: the AI tool now includes protein pairingThe database of 200 million protein-structure predictions now includes homodimers, adding new biological relevance. 13521
Reposted by YC LinNick Polizzi @nickpolizzi.bsky.social · 11/03/2026Our paper with @sokrypton.org using AlphaFold2 to predict small-molecule binding sites in proteins is now out in Nature Methods! 🧵 rdcu.be/e7SnX www.nature.com/articles/s41...rdcu.beAF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2Nature Methods - AF2BIND is a logistic regression model trained on AlphaFold2 pair features to predict small-molecule binding-site residues in proteins, without multiple sequence alignments,... 16921
Reposted by YC LinKate Michie @kmichie.bsky.social · 11/03/2026Nice resource! Thanks for making it open access. Check your protein friends people ( and the accompanying paper in Nat. Methods). 🤩🧶🧬 0104
Reposted by YC LinDavid Ho @davidho.bsky.social · 05/03/2026The perfect headline doesn’t exi…engadget.comGoogle pledges roughly three hours of its annual profit to fight climate changeGoogle and others are committing $100 million to combat climate change. 3075332184
Reposted by YC LinDaniela Barillà @danielabarilla.bsky.social · 11/02/20261610 Marie Curie postdoctoral fellowship awarded out of 17066 applications. Over 50,000 reviewers… Can you fathom the amount of work involved? And sadly the level of waste? 072
Reposted by YC LinProtein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 12/02/2026By 2028, all 4-character PDB IDs will be exhausted. After that, all new entries will receive extended IDs: 12 characters total, formatted as pdb_ + 8 alphanumeric characters (pdb_1000axyz) Test it from PDB Beta Archive Read more: www.wwpdb.org/news/news?ye... 02214
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 11/02/2026Penultimate talk of the meeting by Lauren Porter. Looking at how AlphaFold works under the hood with fold switching proteins. 0123
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 11/02/2026First speaker. Last session at Lorne Proteins. Michael Hecht on designing proteins for novel functions @lorneproteins.bsky.social 074
Reposted by YC LinBrett Collins @brettcollins.bsky.social · 09/02/2026Emily Furlong (UQ alumnus 😄) talking about her new work on ABC transporters. @emfurlong.bsky.social @lorneproteins.bsky.social 1174
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 09/02/2026Closing Session 6: Simon Newstead - Animal to Atom: New avenues for targeting chronic pain. Solute carrier signalling - signaling solute concentrations. Model 1 - e.g. No substrate, lumen ion conc changes. Transporter stabilises, permitting binding TASL, scaffolding its folding. #lorneproteins2026 162
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 09/02/2026Closing Session 4 - Ben Corry - on Membrane transporter plasmodium falciparum Formate Nitrate transporter - moves lactate and protons out of the cell. Detoxification of glycolysis products. Transporter or channel?? Central His highly conserved. #lorneproteins2026 3143
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 08/02/2026Closing Session 3: Elitza Tocheva - Inner to Outer membrane remodelling. Sporulation in Firmicutes cryoET of sporulation. Asymmetric septum, engulfment, spore formation. Second outer spore membrane is lost during germination... #lorneproteins2026 572
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 08/02/2026Fabien Munder - New strategies to fight AMR. Bacterial competition via L-type pyocins; targeting (1) BamA EC loop 6, (2) beta-strand 1. Inhibit beta barrel assembly by blocking the BAM barrel lumen. Increase cell permeability - holes in the OM. 👏 (EMReady post-processing) 🤓 #lorneproteins2026 0105
Reposted by YC Lincorrylab.bsky.social @corrylab.bsky.social · 02/02/2026Beginning 2026 with a flipping good paper🚀 OSCA/TMEM63 proteins do double duty: they’re ion channels and mechanically activated lipid scramblases helping reshape membranes and survive mechanical stress. 👏 @yiechanglin.bsky.social @charlesdcox.bsky.social doi.org/10.1038/s414... 01710
Reposted by YC LinANU Research School of Biology @biologyanu.bsky.social · 02/02/2026Join us on campus & online on Monday, 16 Feb 2026 at 1pm for a seminar by Ciara Wallis, PhD Candidate @corrylab.bsky.social! Details: biology.anu.edu.au/news-events/....biology.anu.edu.auBSB PhD Exit Seminar: Mechanisms of membrane transport proteins borderline between transporters and channelsThroughout my PhD, I determined the transport mechanisms of two proteins that we show break the standard channel / transporter definitions and instead function as anion “chansporters” - proteins that exist somewhere on the spectrum between transporters and channels. 063
Reposted by YC LinARC Tracker @arc-tracker.bsky.social · 20/01/2026Here’s @jsresearchpro.bsky.social reporting on ridiculous new ARC grant time-scales (e.g. 16 months for DPs). The ARC “did not respond to questions about the reasons for the length of the delays or on how the changes will affect researchers’ planning”. I reckon they haven’t thought that far ahead.researchprofessionalnews.comNew ARC grant timescales ‘completely unworkable’ - Research Professional NewsAustralian Research Council cites security checks as reason for major delays to grant outcomes 33618
Reposted by YC LinAdam Kucharski @adamjkucharski.bsky.social · 13/01/2026Want to get the data out of a PDF figure? As in, the actual data – not a rough trace-along-the-lines version? I made an app you might like: adamkucharski.github.io/pdf2plot/ It all started a few years ago... 🧵 18479182
Reposted by YC LinScience Magazine @science.org · 11/01/2026In 2024, researchers in #ScienceRobotics followed up on their development of Third Thumb—a robotic appendage that, when trialed by members of the general public, was a big hit. Learn more: scim.ag/3LmQ9oL #ScienceMagArchives 29724
Reposted by YC LinDr Hannah Murray @hlmurray.bsky.social · 12/01/2026Mind bogglingly awful. It shouldn’t take a year+ to find out if you have a grant. This is careers and lives being messed with. 1198
Reposted by YC LinJournal of Cell Biology @jcb.org · 05/01/2026Sebinelli, Syska, Razmazma et al. @umontpellier.bsky.social show that the yeast protein Ist2, which localizes to ER–PM contact sites, possesses a #phospholipid scramblase activity in its ER-localized transmembrane domain that is important for several ER-related processes. rupress.org/jcb/article/... 0114
Reposted by YC LinPhill Stansfeld @pstansfeld.bsky.social · 25/12/2025🌟 New Tool Alert! We present MemPrO – a toolkit for orienting and building membrane protein systems: ✅ Membrane protein orientation ✅ Mixed membrane building ✅ Double membranes & curvature ✅ Peptidoglycan cell wall support 🔗 github.com/pstansfeld/mempro 📖 pubs.acs.org/doi/10.1021/...pubs.acs.orgMemPrO: A Predictive Tool for Membrane Protein OrientationMembrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi... 04913
Reposted by YC LinLorne Proteins @lorneproteins.bsky.social · 23/12/2025Lorne Proteins 2026 🏖️🤩 Featuring speakers Elitza Tocheva, UBC, on outer spore membrane biogenesis for endospore formation in Firmicutes; and EMBO keynote speaker David Drew, Stockholm University, focusing on GLUT glucose transporters and Na⁺/H⁺ exchangers. 🔗 Register now at: www.lorneproteins.org 0106
Reposted by YC LinChris Mulligan @chrismulligan.bsky.social · 17/12/2025🚨My lab is hiring a postdoc!🚨 If you’re interested in working out the mechanism and physiological impact of bacterial lipid transport processes then please apply! Job advert is here: tinyurl.com/4swddfda Get in touch by email (c.mulligan@kent.ac.uk) for informal enquiries Please repost! Thanks! 1117
Reposted by YC Linsarah mccarry @sarahmccarry.bsky.social · 01/12/2025be the bitch doing something yourself that you want to see in the world 1548231589
Reposted by YC LinThe Conversation U.S. @us.theconversation.com · 26/11/2025Relying on ChatGPT to teach you about a topic leaves you with shallower knowledge than Googling and reading about it, according to new research that compared what more than 10,000 people knew after using one method or the other. Shared by @gizmodo.com: buff.ly/yAAHtHq 12514
Reposted by YC LinPhill Stansfeld @pstansfeld.bsky.social · 24/11/2025Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex. 0154
Reposted by YC LinARC Tracker @arc-tracker.bsky.social · 23/11/2025ARC says they’ll announce DECRA and LIEF outcomes tomorrow (Tuesday 25th Nov). In recent times these announcements have been around 11am Canberra time. With 2 schemes on the same day, I assume they’ll announce one of them later in the day (probably DECRA first). 75926