Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)

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/

Same predicted complex, different confidence scores: ipTM: 0.38 ipSAE: 0.75 Why can these metrics differ? Full breakdown 👇 youtu.be/k4yBqddtPyQ #AlphaFold #AFDB

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 🥳

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

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...

www.pnas.org/post/journal...

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...

pnas.org

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...

Fixed it

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.

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 🧪

‘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?

go.nature.com

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...

My Peer Review of The 1%

I wanted to like QED's new 1% ranking. I don't.

open.substack.com

Time from submission to acceptance: 3 UK Prime Ministers.

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...

Some very cool simulations, look at those little guys climb that ladder! #MolecularNodes

@corrylab.bsky.social · 4mo ago

Excited to share this paper from @yiechanglin.bsky.social showing how lipids can move between bacterial membranes along the bridge like protein TamB. Also happy to be able to post the cool movie. 🎥🌟 #MDsimulations #StructuralBiology doi.org/10.1016/j.bp...

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

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...

phys.org

AlphaFold database now includes 1.7 million 'homodimers' - comprising two interacting strands of the same molecule go.nature.com/4cSmbnT

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.

go.nature.com

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...

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,...

rdcu.be

Nice resource! Thanks for making it open access. Check your protein friends people ( and the accompanying paper in Nat. Methods). 🤩🧶🧬

Nick Polizzi@nickpolizzi.bsky.social · 6mo ago

A public database of binding-site predictions in the human proteome and a google colab notebook to use the model yourself can be found here: github.com/sokrypton/af...

The perfect headline doesn’t exi…

Google pledges roughly three hours of its annual profit to fight climate change

Google and others are committing $100 million to combat climate change.

engadget.com

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?

José Cerca@naturalselection.bsky.social · 7mo ago

Let's look at some numbers 2022: 7 044 applications submitted. 17.9 % success rate 2023: 8 039 applications submitted. 15.8 % success rate 2024: 10 360 applications submitted. 16.6 % success rate 2025: 17 058 applications submitted (record high). 9.7% success rate (preliminary numbers).

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...

Penultimate talk of the meeting by Lauren Porter. Looking at how AlphaFold works under the hood with fold switching proteins.

First speaker. Last session at Lorne Proteins. Michael Hecht on designing proteins for novel functions @lorneproteins.bsky.social

Emily Furlong (UQ alumnus 😄) talking about her new work on ABC transporters. @emfurlong.bsky.social @lorneproteins.bsky.social

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

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

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

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