Tom Mulvaney

How can AI and #cryoEM help save some of the biggest babies on the planet? 🐘🔬

Our new preprint identifies Elephant Herpesvirus gH/gL/gO as a receptor-binding complex and a promising vaccine candidate, now being tested in young elephants across European zoos! 💉

www.biorxiv.org/content/10.6...

New #cryo-EM #preprint- 'Structural mechanisms of drebrin-mediated F-actin network modulation'. Weilong impressively classified out two small #actin binding domains competing for the same surface on #F-actin, one of which also exists in two conformations! #drebrin

www.biorxiv.org/content/10.6...

CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!

R1260 CASP target, water and ions around RNA. Ground truth on left, blind prediction from SoutheRNA MD simulations on right.

#MD blind predictions of water/ions around Tetrahymena ribozyme #RNA matched cryo-EM data better than our baselines! Congrats #CASP16 + @rachael-kretsch.bsky.social + 23 brave groups. Still a ways to go — time for #DeepLearning of water? Community paper: doi.org/10.1002/prot...

Also the slices in Fig S2A look reasonable, but totally different to any slice that would come from the deposited maps.

There are a few including the new Q-score - and this structure might have the lowest Q-score: 0.006 😱

Could it be that the authors uploaded the wrong map and completely ignored the validation report? Seems crazy.

Our Nobel Prize predictions for the next week. #Nobel2025

I really enjoyed the Guggenheim in Bilbao. Richard Serras 'The Matter of Time' made me feel like I was walking inside a cryo-ET reconstruction of a strange cell.

```
import string
alphabet = string.ascii_uppercase
```

I don't think this saves many keystrokes, but it helps if you forgot the alphabet :P

Nanoengineered bioanode with oxygen-insensitive hydrogenase for sustainable energy harvesting from atmospheric hydrogen and waste gases Enzymatic biofuel cells (EBFCs) utilizing hydrogenases to oxidize hydrogen offer a sustainable approach to energy conservation. However, the oxygen se…

1/3 Electricity from air! In the top journal Nano Energy today, we report the first fuel cell that makes power from air alone. We achieved this by using the enzyme Huc to oxidize ambient hydrogen. This results in a continuous low-level power from air and higher outputs with industrial waste gases.

We just bumped into something very preliminary… but very exciting:

AF2.3 and AF3.0 distograms may potentially reproduce MD-like behavior.

Until we do further tests, you can reach our early insights at www.biorxiv.org/content/10.1...

Antidepressants or Tolkien's character?

This amused me: antidepressantsortolkien.vercel.app
I scored 13/24.

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant | PNAS The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capi...

The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant
doi.org/10.1073/pnas...

[Following: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon doi.org/10.1038/s414...

Is this not a reference/citation language issue, rather than a markup/typesetting language issue?

CSL (Citation Style Language) supports a bunch more types than what bibtex offers: docs.citationstyles.org/en/stable/sp...

But now your references are in XML 🤢

Time to retire Alice and Bob?

Is this the first time in history anyone has used 'betwixt' and '2D classes' in the same sentence?

So Germany, I'd really appreciate it if you didn't follow the US lead and fall into darkness today. Thank you.
#Bundestagswahl2025

AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network Advances in machine learning have transformed structural biology, enabling swift and accurate prediction of protein structure from sequence. However, challenges persist in capturing sidechain packing,...

Watch out for an upcoming bluetorial/tweetorial on this work from the amazing @alisiafadini.bsky.social!

www.biorxiv.org/content/10.1...

Some very cool stuff from the group now in paper form:

“ModelArchive: a deposition database for computational macromolecular structural models”
doi.org/10.1016/j.jm...

And

“Comparing macromolecular complexes - a fully automated benchmarking suite” doi.org/10.21203/rs.... (under review)

Have protein-ligand co-folding methods moved beyond memorisation? Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with other molecules, especially small mo...

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹!

www.biorxiv.org/content/10.1...

🧵👇 (1/n)

Check out our new study on water networks in high resolution cryo-EM RNA data!
@ Chiu Lab @ Das Lab

Disturbing. How am I supposed to sleep after watching this.