A guide to types of science papers: Research articles, review papers, & more YouTube video by the bumbling biochemist

A guide to types of science papers: Research articles, review papers, & more
youtu.be/s1t53f9mrLM

Great work Sukrit!

Diagram titled ‘Protein–Drug Prediction Task Breakdown’ showing a hierarchical tree of modeling tasks. Top branches include apo monomer and protein–protein interactions, with sub-branches such as ensembles, induced-fit models, multimers, folded–unfolded complexes, and protein–ligand complexes with mutation effects on binding. Additional branches include potency, ADMET properties (e.g., solubility and blood–brain barrier penetration), and kinetics (e.g., koff). A legend indicates model maturity levels: solid lines (established), dashed lines (promising), and dotted lines (untapped).

More protein-ligand data are needed for AlphaFold-like models (& AI/ML) to enable prospective design!

Check out our piece in "Current Opinion in Structural Biology" – Equal parts a thank-you-letter to the PDB & summarizes how datasets will enable task-focused models!

Link: doi.org/10.1016/j.sb...

A drawing of a dragon that is designed to resemble the autism infinity symbol. The dragon has a serpentine body like that of a Chinese dragon, has rainbow-coloured scales and mane and is on a black background.

It's that time of year again.

Happy autism acceptance month!

The University of Waterloo is seeking internationally renowned scholars, especially those working in #CryoEM, for the prestigious Canada Impact+ Research Chairs program- Chairs receive long-term funding & institutional support - Learn More zurl.co/JBfJ9

I used PyMOL, PDB, Schrödinger, CryoSPARC, and GROMACS plus cryo-EM training at Rutgers and Jefferson to make this all happen! I am now looking for work as I continue creating my own machines (:

The hardest part of science is posing the right question, not answering it.

added a hotkey pair ("," & ".") to incrementally & reversibly tweak map brightness

The full text view is now available, so you can scroll through without needing to download the PDF!

Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing
Ankur Garg, Leah Braviner, Armend Axhemi, Brianna Bibel, Leemor Joshua-Tor
bioRxiv 2026.03.23.713669; doi: doi.org/10.64898/202...

Preprint alert – continuation of my grad school work on CK1α-mediated regulation of Argonaute (Ago) YouTube video by the bumbling biochemist

Beyond thrilled to see the continuation of my grad school work in the Leemor Joshua-Tor lab at CSHL. Huge thanks and congratulations to Ankur Garg, for spearheading the sequel and the whole crew (Leah Braviner, and Armend Axhemi) for getting the work to this point. youtu.be/VzaQUsB1Jlg

The deadline to register for the 2026 Cryo-ET Workshop has been extended extended to April 10! Learn more about this hands-on workshop and apply at: myumi.ch/lsi-cryo-workshop-2026
@jbquerido.bsky.social @shyamalm.bsky.social

"Once you eliminate the impossible, whatever remains, no matter how improbable, must be the truth.”

Quite a few seemingly improbable hypotheses when Verena ‪@vcmentowski.bsky.social‬ started the project

Single-handedly, she dissected the kinetochore corona assembly mechanism.

Congratulations!

Added custom menus, including one to quickly add common monomers (detergents, buffers etc):

screenshot of a resignation letter expressing sadness at leaving NASA

My resignation letter

PDB101: Take the RCSB PDB Survey and Win PDB-101: Training, Outreach, and Education portal of RCSB PDB

Take the RCSB PDB Survey and Win
Share your feedback on Computed Structure Model and IHM usage and enter into a drawing for a Molecular Landscape canvas

The next #CryoEM Current Practices Webinar speaker will be by Rashmi Panigrahi from Memorial University of Newfoundland, St. John’s, Canada speaking on "Capturing Chromatin Dynamics During the DNA Damage Response" 3/26/2026 at 12 PM ET / 9AM PT.

Register today: us02web.zoom.us/webinar/regi...

The 1st UCSC Cryo-EM Workshop - an intensive, hands-on program dedicated to Single Particle Analysis (SPA) will take place June 23–26 at the UCSC Biomolecular Cryo-EM Facility in Santa Cruz, California - Registration closes April 10th - Learn More -> zurl.co/FE5a4

I defended my PhD 10 years ago today. That was the least remarkable thing that happened that day. Sharing something I wrote about it last year. Since then "the horrors persist but so do we." And with dignity.

Apply now! The 2026 call for the EMBO Young Investigator Programme is now open with a deadline of 1 April 12:00 midday CEST. 🧪

More info here:
www.embo.org/funding/fellowships-gran...
#LifeSciences #research #funding

Happy 30th birthday to this paper published March 22, 1996, one of the studies that moved chromatin biology from correlation toward mechanism. Brownell et al. linked a transcription-associated Tetrahymena HAT to yeast Gcn5p, providing a biochemical link for chromatin modification to gene activation.

1) The Herzik lab is excited to announce our newest preprint in collaboration with the Grotjahn lab! We have developed a surfactant cocktail that seeks to overcome one of the more nefarious problems in #cryoEM, Air-water interface (AWI)-induced damage and preferred orientation (PO).

Also added a hotkey "C" to auto-resample EM maps, & "G" to toggle between a global, solid-surface view of an EM map and a local clipped mesh. There are also keys to adjust opacity which only adjust the opacity of the surface (and the toggle remembers the opacity when you switch back):

Finally got around to porting my coot-trimmings scripts over to Coot 1... only the hotkeys are working (nothing requiring creating a custom menu or GUI dialog), but I've added a couple of new ones, e.g. copy/pasting ligands.

Check it out & let me know what you think! 😊

github.com/olibclarke/c...

GitHub - BigDataBiology/GMSC-mapper Contribute to BigDataBiology/GMSC-mapper development by creating an account on GitHub.

We released GMSC-mapper v0.2.0! GMSC-mapper queries the Global Microbial smORFs Catalog to find and annotate small proteins from metagenomic data

github.com/BigDataBiolo...

this is a crisis.

👇👏👇👏👇👏👇👏

Enhancing interpretability of cryo-EM maps with hybrid attention Transformers www.biorxiv.org/content/10.64898/2026.01...