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YC Lin

@yiechanglin.bsky.social
916 followers 832 following 22 posts

Boya Postdoctoral Fellow @PKU | formally Corry Lab, ANU MD simulations of lipids and membrane proteins Like PIP2, I am negatively charged in the head

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Reposted by YC Lin
Philippe Le Mercier, ViralZone @viralzone.bsky.social · 22/09/2026
A 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/...
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Alexis Verger 🧬🧫🧪 @alexis-verger.cpesr.fr · 21/09/2026
Nice talk, really perfect for teaching Everything you've always wanted to know about #AlphaFold, iPTM, PAE, pLDDT, and ipSAE but were afraid to ask
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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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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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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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Kumaran Ramamurthi @ramamurthilab.bsky.social · 15/09/2026
How 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.org
PNAS
Proceedings 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...
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 13/09/2026
Fold 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/
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 10/09/2026
Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB
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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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corrylab.bsky.social @corrylab.bsky.social · 01/09/2026
Excited 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
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/08/2026
Run 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...
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Robert Arkowitz @robertarkowitz.bsky.social · 18/08/2026
www.pnas.org/post/journal...
pnas.org
Probes show lipids are far more selective for proteins than once thought
Lipids, 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...
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henrietteautzen.bsky.social @henrietteautzen.bsky.social · 12/08/2026
Happy 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...
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Christophe 🔬 Leterrier @christlet.bsky.social · 11/08/2026
Fixed it
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Stephanie Wankowicz @stephanieaw.bsky.social · 11/08/2026
Most 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.
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Nature Portfolio @natureportfolio.nature.com · 06/08/2026
Review 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 wars
Review 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?
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Ran Blekhman @blekhman.bsky.social · 27/06/2026
I 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.com
My Peer Review of The 1%
I wanted to like QED's new 1% ranking. I don't.
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Oded Rechavi @odedrechavi.bsky.social · 23/06/2026
Time from submission to acceptance: 3 UK Prime Ministers.
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Reichow Lab @reichowlab.bsky.social · 01/06/2026
Dual-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...
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Brady Johnston @bradyajohnston.bsky.social · 28/05/2026
Some very cool simulations, look at those little guys climb that ladder! #MolecularNodes
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Kate Michie @kmichie.bsky.social · 09/04/2026
Our 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.social
phys.org
From Asgard to Earth: Tiny tubes may reveal the moment complex life began
Stromatolites—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...
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Nature @nature.com · 17/03/2026
AlphaFold database now includes 1.7 million 'homodimers' - comprising two interacting strands of the same molecule go.nature.com/4cSmbnT
go.nature.com
AlphaFold hits ‘next level’: the AI tool now includes protein pairing
The database of 200 million protein-structure predictions now includes homodimers, adding new biological relevance.
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Nick Polizzi @nickpolizzi.bsky.social · 11/03/2026
Our 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.be
AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2
Nature 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,...
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Kate Michie @kmichie.bsky.social · 11/03/2026
Nice resource! Thanks for making it open access. Check your protein friends people ( and the accompanying paper in Nat. Methods). 🤩🧶🧬
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David Ho @davidho.bsky.social · 05/03/2026
The perfect headline doesn’t exi…
engadget.com
Google pledges roughly three hours of its annual profit to fight climate change
Google and others are committing $100 million to combat climate change.
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Daniela Barillà @danielabarilla.bsky.social · 11/02/2026
1610 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?
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Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · 12/02/2026
By 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...
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Lorne Proteins @lorneproteins.bsky.social · 11/02/2026
Penultimate talk of the meeting by Lauren Porter. Looking at how AlphaFold works under the hood with fold switching proteins.
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Lorne Proteins @lorneproteins.bsky.social · 11/02/2026
First speaker. Last session at Lorne Proteins. Michael Hecht on designing proteins for novel functions @lorneproteins.bsky.social
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Brett Collins @brettcollins.bsky.social · 09/02/2026
Emily Furlong (UQ alumnus 😄) talking about her new work on ABC transporters. @emfurlong.bsky.social @lorneproteins.bsky.social
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Lorne Proteins @lorneproteins.bsky.social · 09/02/2026
Closing 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
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Lorne Proteins @lorneproteins.bsky.social · 09/02/2026
Closing 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
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Lorne Proteins @lorneproteins.bsky.social · 08/02/2026
Closing 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
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Lorne Proteins @lorneproteins.bsky.social · 08/02/2026
Fabien 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
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corrylab.bsky.social @corrylab.bsky.social · 02/02/2026
Beginning 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...
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ANU Research School of Biology @biologyanu.bsky.social · 02/02/2026
Join 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.au
BSB PhD Exit Seminar: Mechanisms of membrane transport proteins borderline between transporters and channels
Throughout 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.
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ARC Tracker @arc-tracker.bsky.social · 20/01/2026
Here’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.com
New ARC grant timescales ‘completely unworkable’ - Research Professional News
Australian Research Council cites security checks as reason for major delays to grant outcomes
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Adam Kucharski @adamjkucharski.bsky.social · 13/01/2026
Want 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... 🧵
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Science Magazine @science.org · 11/01/2026
In 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
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Dr Hannah Murray @hlmurray.bsky.social · 12/01/2026
Mind bogglingly awful. It shouldn’t take a year+ to find out if you have a grant. This is careers and lives being messed with.
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Journal of Cell Biology @jcb.org · 05/01/2026
Sebinelli, 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/...
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Phill 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.org
MemPrO: A Predictive Tool for Membrane Protein Orientation
Membrane proteins play a vital role in numerous cellular processes, including ion transport, intercellular communication, and antibiotic resistance. Ensuring their accurate orientation within lipid bi...
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Lorne Proteins @lorneproteins.bsky.social · 23/12/2025
Lorne 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
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Chris 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!
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sarah mccarry @sarahmccarry.bsky.social · 01/12/2025
be the bitch doing something yourself that you want to see in the world
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The Conversation U.S. @us.theconversation.com · 26/11/2025
Relying 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
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Phill Stansfeld @pstansfeld.bsky.social · 24/11/2025
Super collaboration with @raffaeleieva.bsky.social and @fronzeslab.bsky.social on the LptDEMY complex.
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ARC Tracker @arc-tracker.bsky.social · 23/11/2025
ARC 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).
Screenshot of tweet from the ARC saying they’ll announce DECRA and LIEF outcomes on Tuesday 25th Nov.
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