Oli Clarke

Images of molecular models of ALG3 and ALG9 proteins with substates bound.

I’m very excited to share some newly published work that uncovers the molecular basis for oligomannose synthesis!

www.nature.com/articles/s41...

Thank you!! My first time at ASBMB, great meeting so far! 😊

Figure 1. Cryo-EM of abundant protein complexes in native membranes.

Figure 2. Cryo-EM of membrane proteins in vesicles.

Figure 3. 3D reconstruction of V-ATPase in native synaptic vesicle membranes.

Figure 4. Generation of membrane vesicles for structure determination of proteins in their native lipid bilayer.

I've written a review on what I think is an extremely exciting direction in cryo-EM:

Cryo-EM of endogenous membrane proteins in their native lipid bilayer

Open access in Quarterly Reviews of Biophysics:
doi.org/10.1017/S003...

Thank you Sjors and congrats to you & Sofia on your beautiful vault work!! 🙏 maps/PDBs are out, and movies should be on EMPIAR soon 😊

6/10 Notable finds: Asgard archaeal homologues of the Vault (MVP) complex and the Commander (COMMD) complex — two eukaryotic assemblies whose prokaryotic origins were previously unknown.
Multimer modelling predicts ring-shaped homo-oligomers in both cases. 🏛️

Is this still available Alexis? Link seems dead... I know a candidate who might be a good fit

Trimbody with rigid AI-designed scaffolds enables atomic-resolution cryo-EM structure determination of small proteins pubmed.ncbi.nlm.nih.gov/41735342/ #cryoEM

The giant viruses surprised us at almost every turn of this project, but ultimately led us down a very rewarding path. Happy to share this work is now available online 🧪

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

Metadynamics meets diffusion-based structure prediction: the same trick that drives enhance sampling of MD trajectories can be adapted and applied as steering terms during generation to sample diverse conformations. Seems obvious in hindsight!

Image of a herpesvirus structure

I am excited to share our latest preprint - An evolutionarily divergent herpesvirus with a giant tail. Featuring symmetry breaking and genome annotation from structure using ModelAngelo. doi.org/10.64898/202...

Structure-guided design of a targeted autoantibody degrader for neurologic disease pubmed.ncbi.nlm.nih.gov/41676581/ #cryoEM

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

How could a simple self-replicating system emerge at the origins of life? RNA polymerase ribozymes can replicate RNA, but existing ones are so large that their self-replication seems impossible. Could they be smaller?

Excited to share our latest work in @science.org on a new small polymerase.
1/n

Yes but on biorxiv since 2024

AlignPCA-2D: PCA-Reduced Euclidean Vector Alignment for 2D Classification in Cryo-EM https://www.biorxiv.org/content/10.64898/2026.02.11.705027v1

Yep that one works, cool stuff!

this looks super cool but the DOI is not resolving!

Some cool E3 ligase structures here with calmodulin-mediated oligomerisation. Also interesting collection/processing to deal with preferred orientation.

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

Molecular mechanisms of flotillin complexes in organizing membrane microdomains pubmed.ncbi.nlm.nih.gov/41663364/ #cryoEM

Structural basis of caveolin-driven membrane bending https://www.biorxiv.org/content/10.64898/2026.02.05.703862v1

Introducing The Structural History of Eukarya (SHE): The first proteome-scale phylogeny constructed entirely from 3D structure.
We computed 300 trillion alignments across 1,542 species to map the tree of life. 🧵👇 (1/5)

GitHub - bytedance/Protenix: Toward High-Accuracy Open-Source Biomolecular Structure Prediction. Toward High-Accuracy Open-Source Biomolecular Structure Prediction. - bytedance/Protenix

Protenix v1.0 is out with some very impressive performance numbers (exceeding AF3 performance on protein-protein complexes)

Robust quality assessment of cryo-EM maps, tomograms and micrographs by statistics-based local resolution estimation https://www.biorxiv.org/content/10.64898/2026.02.03.703505v1

Molecular insights into the capsular polysaccharide transporter Wza-Wzc complex pubmed.ncbi.nlm.nih.gov/41644548/ #cryoEM

This just in. So honored and grateful...

Huh - a trimeric aquaporin, that is unexpected (although per the paper, apparently predictable by AF3)

FILED January 31, 2026 CLERK, U.S. DISTRICT COURT WESTERN DISTRICT OF TEXAS Jaemie Herndon DEPUTY ADRIAN CONEJO ARIAS, and L.C.R., a Minor Child by and through His Parent and Guardian Adrian Conejo Arias, Petitioners, VS. KRISTI NOEM, in Her Official Capacity as Secretary of the United States Department of Homeland Security; PAMELA BONDI, in Her Official Capacity as Attorney General of the United States; TODD LYONS, in His Official Capacity as Acting Director, United States Immigration and Customs Enforcement; DAREN MARGOLIN, in His Official Capacity as Acting Director of the Executive Office of Immigration Review; and JOHN DOE, in His Official Capacity as the Warden of the Dilley Immigration Processing Center in Dilley, Texas, Respondents. CIVIL CASE NO. SA-26-CV-415-FB § OPINION AND ORDER OF THE COURT

Civics lesson to the government: Administrative warrants issued by the executive branch to itself do not pass probable cause muster. That is called the fox guarding the henhouse. The Constitution requires an independent judicial officer. Accordingly, the Court finds that the Constitution of these United States trumps this administration's detention of petitioner Adrian Conejo Arias and his minor son, L.C.R. The Great Writ and release from detention are GRANTED pursuant to the attached Judgment. Observing human behavior confirms that for some among us, the perfidious lust for unbridled power and the imposition of cruelty in its quest know no bounds and are bereft of human decency. And the rule of law be damned.

Ultimately, Petitioners may, because of the arcane United States immigration system, return to their home country, involuntarily or by self-deportation. But that result should occur through a more orderly and humane policy than currently in place. Philadelphia, September 17, 1787: "Well, Dr. Franklin, what do we have?" "A republic, if you can keep it." With a judicial finger in the constitutional dike, It is so ORDERED. SIGNED this 31st day of February [sic], 2026. Fred Biery FRED BIERY UNITED STATES DISTRICT JUDGE Credit: Bystander Matthew 19:14 John 11:35

BREAKING: Federal judge orders Adrian Conejo Arias and his minor son, L.C.R., released.

"The Great Writ and release from detention are GRANTED."

"Civics lesson to the government: Administrative warrants issued by the executive branch to itself do not pass probable cause muster."

Judge Biery signed the order with a photo of Liam and two bible verses: The first is "But Jesus said, Suffer little children, and forbid them not, to come unto me: for of such is the kingdom of heaven." The second is simply "Jesus wept."

Astonishing thing for a judge to do.

Formation & function of #MembranelessOrganelles! #CryoET structures of #proteasome storage granules inside cells!
Read our paper @cp-cell.bsky.social!

❕Publication: doi.org/10.1016/j.ce...
❕Press Release: www.biochem.mpg.de/en/pressroom

@uoftmedicine.bsky.social
@erc.europa.eu #UPSmeetMet

Yeah - but if it works where nothing else did, it's only one day, and you can proceed to local refinement from there 🤷🏻‍♂️