iiinova — where your digital self keeps evolving

Reposted by Martin Rennie

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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Yuan He @yuanhejhu.bsky.social · 22/09/2026

A big week for the lab! Two new papers on how cells repair DNA double-strand breaks: one on getting NHEJ started in chromatin, one on processing the ends before ligation. Years of work by a fantastic team.

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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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EMBL @embl.org · 15/09/2026

Scientists have determined the highest-resolution protein structure obtained to date. Using advanced X-ray crystallography techniques at EMBL Hamburg's P14 beamline, the team solved the structure of an archaeal protein at an astonishing 0.43 Ångström resolution. www.embl.org/news/science...

embl.org

Every electron counts: most detailed protein structure to date revealed | EMBL

Researchers have used advanced X-ray crystallography methods to determine the structure of an archaeal protein at unprecedented resolution

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Reposted by Martin Rennie

Richard Sever @richardsever.bsky.social · 26/06/2026

“the academic community is enormously heterogeneous and it’s almost impossible to keep everyone happy” Never a truer word said in this analysis of downstream consequences of openness by @jacoates.bsky.social ripplingideas.org/2026/06/26/t...

ripplingideas.org

The 1% club and the rocky road ahead for bioRxiv

The recent launch of qed’s “top 1%” preprint ranking has sparked controversy, with concerns about its arbitrary nature, potential harm to authors, and low-quality inclusions. Whil…

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Reposted by Martin Rennie

cryoEM papers @cryoempapers.bsky.social · 26/06/2026

Caveat emptor: predicting and modeling protein-DNA recognition and binding via machine-learning computational approaches pubmed.ncbi.nlm.nih.gov/42345194/ #cryoEM

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Reposted by Martin Rennie

cryoEM papers @cryoempapers.bsky.social · 11/06/2026

Atomic resolution cryo-EM at 200 keV pubmed.ncbi.nlm.nih.gov/42268577/ #cryoEM

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Marcin J. Suskiewicz @msuskiewicz.eurosky.social · 21/05/2026

I wrote a blog on metaphors that I find useful for ''the age of AI' msuskiewicz.github.io/blog/

msuskiewicz.github.io

Blog

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Sholto David @sholtodavid.bsky.social · 17/05/2026

Surprised to discover that Thermo Fisher appears to show a fake western blot for the validation of one of their p53 antibodies. I've added a diagram to show the very similar bands. This does not appear to be one of the "published figures" but their own internal data.

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Reposted by Martin Rennie

Martin Pacesa @martinpacesa.bsky.social · 29/04/2026

I am happy to share a review I recently wrote on the design of peptide binders. It gives an overview of experimentally validated tools and discusses the challenges of why peptide design is more difficult than the design of classical protein binders. www.chimia.ch/chimia/artic...

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Reposted by Martin Rennie

scmicryoem.bsky.social @scmicryoem.bsky.social · 24/04/2026

On the train back from yet another excellent @ccpem.bsky.social Spring Symposium. It was excellent to catch up with many friends, collaborators and vendors and the talks have given us plenty of ideas for the facility that we can improve and implement for our users. Until next year!

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Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 22/04/2026

Calling all xray structure folks that have worked with denovo proteins. Do you suffer from high rfactors? Myself, someone else I know and now multiple structures all seem to suffer from this. Assuming we all tried our best in model building, what could be some causes?

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Torsten Schwede @torstenschwede.bsky.social · 13/03/2026

Is #AI hitting a plateau in structure prediction? Help us find out at CASP17! 🧪🧬 Calling for Targets: Immune Complexes, protein - ligand complexes, RNA/DNA, conformational ensembles, membrane proteins, viral origins, and large complexes. The Rule of Thumb: If AF3 can’t model it, we want it.

The Critical Assessment of Structure Prediction (CASP) experiment is calling for prediction targets: Immune Complexes, Organic Ligand-Protein Complexes, Nucleic Acids and Complexes, Conformational Ensembles, Difficult Protein Structures and Complexes.
Rule of Thumb: If AlphaFold3 can generate a high-quality model, it is likely not a CASP-grade challenge. If it struggles, we want it.

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TJ McCorvie @allostericstate.bsky.social · 05/04/2026

2D classes of the 58 kDa sample collected on the 100 keV Tundra TEM with a Falcon C detector at @nusbf.bsky.social @newcastleuni.bsky.social. Still much work to do to optimise the sample & data collection but its cool to see what a 100 keV TEM is capable of. #cryoEM @recon4imd.bsky.social

2D classes of a 58 kDa particle collected on a 100 kev Tundra electron microscope

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cryoEM papers @cryoempapers.bsky.social · 15/03/2026

EEPD1 evolved a unique DNA clamping dimer protecting reversed replication forks pubmed.ncbi.nlm.nih.gov/41830330/ #cryoEM

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Reposted by Martin Rennie

scmicryoem.bsky.social @scmicryoem.bsky.social · 13/03/2026

Last week, we hosted 6 participants on the Cryo-EM in Structural Biology 2026 course, part of our Wellcome/MRC-funded training programme. The course was hybrid with online lectures together with the other hosts and onsite practicals. Find out more: www.gla.ac.uk/research/az/...

6 women and 4 men pose on a staircase with floor-to-ceiling glass on the left side. A pop-up banner promoting the Scottish Centre for Macromolecular Imaging is in the foreground.

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Reposted by Martin Rennie

Leo Kiss @leokiss.bsky.social · 05/03/2026

I am incredibly excited to share that I will start my independent lab at the @unidue-zmb.bsky.social at the @unidue.bsky.social as Junior Professor of Cellular Biochemistry. Research in my lab has the goal to decipher the ubiquitin code! There are multiple open positions! (1/3)

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Martin Rennie @martinrennie.bsky.social · 27/02/2026

Excited to share our new paper uncovering how FANCD2 recognises various DNA repair proteins www.biorxiv.org/content/10.6... @hw1o9.bsky.social

biorxiv.org

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Reposted by Martin Rennie

Roland Dunbrack 🏳️‍🌈 @rolanddunbrack.bsky.social · 17/02/2026

We posted a biorxiv preprint on structural bioinformatics, AlphaFold modeling & machine learning on predicting specificity of E3 ligase ring domains for different E2 enzymes. 1/4 Preprint: www.biorxiv.org/content/10.6... Models/data (UbiqCore website): dunbrack.fccc.edu/ubiqcore

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RCSB Protein Data Bank @rcsbpdb.bsky.social · 02/11/2025

AI in Protein Design: Hype vs. Reality Explained by David Baker In this GEN interview, he emphasizes that designing new proteins from scratch is now a reality. Whether AI transforms medicine will require improving our understanding of biology's complexity

genengnews.com

AI in Protein Design: Hype vs. Reality Explained by David Baker

In this GEN interview, Nobel Laureate David Baker, PhD, emphasizes that designing proteins from scratch is reality and unpacks what's needed for AI to transform medicine.

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Lucas Farnung @lucas.farnunglab.com · 24/10/2025

I love AlphaFold—but please include PAE (Predicted Aligned Error) plots for every “interaction.” Pretty PDBs ≠ proof. If the PAE doesn’t show an interface, it ain’t one. Show the plots. Structural biology's reputation is on the line.

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Adrian Roitberg @adrianroitberg.bsky.social · 23/10/2025

Finally out in print! Long time project with @olexandr.bsky.social and the PHENIX group. Refinement of X-ray and CryoEM structures, using Machine Learned Potentials as the back end to help fitting. This fulfills the old dream of doing QM refinement, but very very cheap www.nature.com/articles/s41...

nature.com

AQuaRef: machine learning accelerated quantum refinement of protein structures - Nature Communications

AQuaRef employs machine learning to refine protein structures from cryo-EM and X-ray data in Phenix. It achieves quantum-level precision, improving model geometry and fit to the data while reducing ov...

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Joe Greener @jgreener64.bsky.social · 15/10/2025

I wrote a blog post about the future of structural bioinformatics. Where to go after AlphaFold? How do we avoid the field becoming a load of half-baked LLMs? Let me know what you think. jgreener64.github.io/posts/struct...

jgreener64.github.io

Where next for structural bioinformatics?

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Gary Stevenson @garyseconomics.bsky.social · 21/09/2025

Will Reform win the next UK election? www.youtube.com/watch?v=mcu0...

youtube.com

Will Reform win the next UK election?

YouTube video by Garys Economics

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Reposted by Martin Rennie

Nate Corley @ncorley.bsky.social · 19/09/2025

RFdiffusion3 is here! We train a general network that explicitly models every atom and use it to design active enzymes and DNA binders. Tremendous team effort with Jasper, Rohith, Raktim, Rafi, Yanjing, Paul, Jonathan, and many others! Check it out: lnkd.in/eiUFfJaM.

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Reposted by Martin Rennie

Oli Clarke @olibclarke.bsky.social · 13/09/2025

This 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

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Sebastian Deorowicz @sdeorowicz.bsky.social · 19/07/2025

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

biorxiv.org

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale

We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

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Julien Capin @ju-cap.bsky.social · 17/07/2025

You designed binders for your favourite protein and wish there was a way to experimentally screen them within 24h w/ only a set of pipettes and a plate reader? Check out our Cell-Free 2-Hybrid approach (CF2H) Full post: tinyurl.com/48cz5nb6 Preprint: www.biorxiv.org/cgi/content/...

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Gary Stevenson @garyseconomics.bsky.social · 13/07/2025

I'm back. Here's how we fix the UK's dire economic and political situation www.youtube.com/watch?v=LMor...

youtube.com

I'm back – and I think we can win

YouTube video by Garys Economics

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Reposted by Martin Rennie

Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 07/07/2025

Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬 📄 www.biorxiv.org/content/10.1... 🌐 search.foldseek.com/folddisco

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Oli Clarke @olibclarke.bsky.social · 02/07/2025

This is quite something - 68% success rate for binder design w/ Chai 2, with many in the low-nM to pM range - impressive stuff chaiassets.com/chai-2/paper...

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Reposted by Martin Rennie

Martin Pacesa @martinpacesa.bsky.social · 30/06/2025

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

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Journal of Cell Biology @jcb.org · 27/06/2025

The E3 ligase Parkin ubiquitinates many proteins. Koszela, Walden (@hw1o9.bsky.social) et al. @uofglasgow.bsky.social‬ identify and biochemically validate a direct Parkin interaction with a substrate, Miro1. rupress.org/jcb/article/...

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Utrecht Virology Lab @utrechtvirology.bsky.social · 18/06/2025

A nifty trick our lab is using to improve structure prediction of viral membrane proteins in #AlphaFold3! 👇

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Andrew Deans @genomestability.bsky.social · 02/06/2025

🧬 New from crystal structures from our lab in EMBO Journal! We reveal how the FANCM enzyme, an emerging therapeutic target it cancer, has evolved to specifically recognise branched DNA and activate the Fanconi anaemia pathway of DNA repair. doi.org/10.1038/s443... 🧵👇

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Iso Hirst @isobelhirst.bsky.social · 02/06/2025

I’m very happy to share my first paper on the effects of AWI interactions and flexibility on SPA data quality! Thank you to everyone on the team 🤩 www.sciencedirect.com/science/arti...

sciencedirect.com

Untangling the effects of flexibility and the AWI in cryoEM sample preparation: A case study using KtrA

Single particle cryo-electron microscopy (cryoEM) is a powerful tool for elucidating the structures of biological macromolecules without requiring cry…

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Arjen Jakobi @cryotud.bsky.social · 22/05/2025

We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation. Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation. cryotud.github.io/locscale/

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Royal Society Publishing @royalsocietypublishing.org · 21/04/2025

New from #JRSocInterface: Emerging frontiers in protein structure prediction following the #AlphaFold revolution. Read more: royalsocietypublishing.org/doi/10.1098/...

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Martin Rennie @martinrennie.bsky.social · 22/04/2025

Our review on #AlphaFold focussing on prediction classes beyond simple protein monomers (PPIs, conformational changes, protein-ligand complexes, etc) royalsocietypublishing.org/doi/10.1098/...

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Yehlin Cho @yehlincho.bsky.social · 08/04/2025

Excited to share our preprint “BoltzDesign1: Inverting All-Atom Structure Prediction Model for Generalized Biomolecular Binder Design” — a collaboration with @martinpacesa.bsky.social, @Zhidian Zhang, @Bruno E. Correia, and @sokrypton.org 🧬 Code will be released in a couple weeks

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ChimeraX @chimerax.ucsf.edu · 06/03/2025

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

Nipah virus G protein with 16813 ligands (mostly waters) mapped from similar structures.

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cryoEM papers @cryoempapers.bsky.social · 23/11/2024

Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 pubmed.ncbi.nlm.nih.gov/39574680/

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Will Fuller @fuller-lab.bsky.social · 16/11/2024

Well, this is exciting. A 5 year postdoc position in my lab. Do ion channels appeal to you? What about calcium? This is going to be such a fun project!👇 my.corehr.com/pls/uogrecru...

my.corehr.com

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