Tom Mulvaney
@tmulvaney.bsky.social
Postdoctoral researcher in the Topf Lab @ CSSB & Leibniz Institute for Virology in Hamburg. Interested in cryo-EM, structural biology, and virology. I like bikes, sometimes I ride them.
Reposted by Tom Mulvaney
#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...
November 11, 2025 at 12:53 AM
#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...
Reposted by Tom Mulvaney
Our Nobel Prize predictions for the next week. #Nobel2025
October 5, 2025 at 5:15 PM
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.
October 4, 2025 at 2:04 PM
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.
Reposted by Tom Mulvaney
Reposted by Tom Mulvaney
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.
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…
www.sciencedirect.com
August 8, 2025 at 3:49 AM
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.
Reposted by Tom Mulvaney
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...
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...
July 29, 2025 at 1:01 PM
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...
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...
This amused me: antidepressantsortolkien.vercel.app
I scored 13/24.
I scored 13/24.
Antidepressants or Tolkien's character?
antidepressantsortolkien.vercel.app
July 29, 2025 at 8:49 PM
This amused me: antidepressantsortolkien.vercel.app
I scored 13/24.
I scored 13/24.
Reposted by Tom Mulvaney
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...
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...
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...
doi.org
July 2, 2025 at 3:27 PM
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...
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...
Reposted by Tom Mulvaney
Time to retire Alice and Bob?
March 25, 2025 at 8:58 AM
Time to retire Alice and Bob?
Reposted by Tom Mulvaney
So Germany, I'd really appreciate it if you didn't follow the US lead and fall into darkness today. Thank you.
#Bundestagswahl2025
#Bundestagswahl2025
February 23, 2025 at 12:22 PM
So Germany, I'd really appreciate it if you didn't follow the US lead and fall into darkness today. Thank you.
#Bundestagswahl2025
#Bundestagswahl2025
Reposted by Tom Mulvaney
Watch out for an upcoming bluetorial/tweetorial on this work from the amazing @alisiafadini.bsky.social!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
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,...
www.biorxiv.org
February 22, 2025 at 8:50 AM
Watch out for an upcoming bluetorial/tweetorial on this work from the amazing @alisiafadini.bsky.social!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Tom Mulvaney
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)
“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)
Redirecting
doi.org
February 21, 2025 at 5:13 PM
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)
“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)
Reposted by Tom Mulvaney
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
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...
www.biorxiv.org
February 8, 2025 at 10:02 AM
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)
www.biorxiv.org/content/10.1...
🧵👇 (1/n)
Reposted by Tom Mulvaney
Check out our new study on water networks in high resolution cryo-EM RNA data!
@ Chiu Lab @ Das Lab
@ Chiu Lab @ Das Lab
January 25, 2025 at 8:01 PM
Check out our new study on water networks in high resolution cryo-EM RNA data!
@ Chiu Lab @ Das Lab
@ Chiu Lab @ Das Lab