I updated ipSAE code to handle Boltz2 files properly -- non-standard chainIDs/order, PDB input as well as mmCIF; other pull requests. github.com/DunbrackLab/.... Also updated preprint--fixed Latin grammar error in title - very embarrassing and added new figure. www.biorxiv.org/content/10.1...

Magic incoming from our team soon....

There are moments in life when certain people nearby just show up for you- no fanfare, no fuss, just pure goodness. And honestly? These people deserve a standing ovation, confetti cannons, and maybe even a parade.

Thrilled to share our PI’s new publication exploring filament ambition of FAM118A/FAM118B in NSMB. These proteins show remarkable self-assembly with clear implications for their biological roles, proving once again that structure n function go hand in hand or in this case, subunit by subunit.

Science just pulled up a chair at the kitchen table: a new paper explores the physics behind droplet outbursts when slicing onions www.pnas.org/doi/10.1073/...

Grateful to be listed as an author in this insightful review. All credits to Marcin Sir for his generosity, considering my contribution was more of a cameo than a lead role.

Let's connct Biology to real life examples Cooperativity: Like applause spreading through a crowd Transient complexes: Like birds flying in formation, then dispersing Affinity: like gravity between planets (weak individually, but strong and inevitable when surfaces complement)

Amazing insights to the phosphorylation world

Beauty of academia- you spend your days with minds trying to understand a basic concept, seeking solutions and not working for profit. That quiet pursuit changes the air you breathe and, eventually, you.

As a PhD student, I've been buried in bits and bytes of structural biology and biochemistry for the past two years and yet honestly I feel like I know absolutely nothing. Take an amino acid residue, for instance.

Science literally got its own taste: doi.org/10.1063/5.02... Einstein would’ve loved this dish. Time, temperature, and relativity- all served al dente!

Trust me, success is finding a team with whom you can laugh with.

Cryo-EM captures the elusive moment when E1 hands off SUMO to E2- a molecular relay that’s been mostly guesswork until now. The structures reveal E1 doing dramatic shape-shifting to line up perfectly for the transfer, like enzyme origami in action.

Today we stepped into world of crystallography with Proxima2 beamline at SOLEIL synchrotron. So what did we learn? Imagine convincing a tiny, perfect crystal to spill its atomic secrets by blasting it with an intense X-ray beam until it diffracts in a very specific, beautiful pattern.

The Angst of Losing Protein Midway: A Protein That Never Made It to the SDS-PAGE. You were so close. Just a few fractions away from your pure, precious protein. You’ve spent days, maybe weeks, growing cultures, lysing cells, spinning lysates, filtering, calibrating columns, babysitting gradients.

Mitophagy receptors’ IDRs trigger ER fragmentation and ER-phagy when transplanted at the ER membrane. www.nature.com/articles/s41...

Today’s serotonin boost? My personal timer appearing while I was making gourmet meals for bacteria. Who needs diamonds when you have surprise lab tools? #PhDlife

I supervise an excellent postdoc who's looking for a postdoc or associate position in < 1 yr. Highly skilled in chem biol and biochem (peptide synthesis, native chem ligation, bacterial expression, purification, intein-based splicing, crystallography, interaction assays). Contact me if interested.

SUMOylation studies just got a serious upgrade! Fresh out of the lab- our team including our brilliant chemist PostDoc just published a clean, streamlined way to purify SUMO E2 and SUMO RANGAP. Whether one is into structural biology or biochemical wizardry, this toolkit is your new best friend.

Amazing work with solid experimental backing and crystal structures. BindCraft is here to stay.

If you are kind, people may accuse you of selfish, ulterior motives. Be kind anyway. If you are successful, you will win some false friends and some true enemies. Succeed anyway. What you spend years building, someone could destroy overnight. Build anyway.

It's all just math... softmax() more specifically (aka "attention" or partition function). The assumption of alphafold is that everything you provide is interacting/folded. As you add more context, the softmax is over larger number of possibilities. (1/2)

Interesting: Cu2+-binding sites on SUMO connecting multiple SUMOs together.

Science truly is amazing. Emperor Akihito of Japan continues to publish scientific papers as first author, proudly listing his unique royal address. Now that’s dedication to research! www.sciencedirect.com/science/arti...

Mechanistic study on RING E3 #ubiquitin ligases in LSA, from @cruk-si.bsky.social comprehensively investigates the role of the linchpin residue. Demonstrating activation of E3 ligase and concepts for protein design, along with a framework for methods. www.life-science-alliance.org/content/8/10...

An example of amino acids driving the cellular machinery...

[Resources] #AlphaFold protein and PPI prediction databases 1️⃣ Predictomes (genome maintenance & H2A/H2b) predictomes.org 2️⃣ Flypredictome www.flyrnai.org/tools/fly_pr... 3️⃣ Human interactome prodata.swmed.edu/humanPPI 4️⃣ BFVD (viral proteins) bfvd.steineggerlab.workers.dev 1/2

Protein biochemistry is amazing—and by amazing, I mean a wild ride that starts with 300 mL of preculture, scales up to 6 liters of shaking culture (that mysteriously always finishes at 2 AM), and hopefully ends with at least 6 grams of cell pellet.

Our lab superstar Stephane takes care of our lab in the best way possible. It's an honor to share the lab with him every single day.

A blend of Science and fun... www.science.org/doi/10.1126/...

Mere color, unspoiled by meaning, and unallied with definite form, can speak to the soul in a thousand different ways. — Oscar Wilde

Academia is a tightly-knit world, one that thrives on traditions, mentorship, and the quiet yet powerful legacy of knowledge passed down through generations. Recently, this came true when my PhD supervisor’s own PhD supervisor @clausenlab.bsky.social visited our team.

This paper will be special thanks to my: -first protein crystal (I may have screamed a little) -first purification (so much buffer) -first ITC experiment (spoiler: it worked!) -first SDS PAGE (a rite of passage, right?) Grateful for the journey, the learning n moments of “wow, I actually did that.”

I was about to go to my Institute for work, but instead went for a long stroll. People were happy, birds were chirping, pets were chilling and water was glistening. Nature! It reminded me of these lines by W.H. Davies: "What is this life if, full of care, We have no time to stand and stare?"

Academia’s a journey of the mind—and sometimes, of clay. When the café that fired your ceramics puts them on display, it feels like a little piece of your soul is seen. So glad the sunshine rangoli sent warm vibes all the way here at France :)

20 tubes of 1 mM protein → 9 tubes of 1.4 mM protein after concentrating the protein. Am unsure if this is supposed to make me happy for the gain or sad for the loss #LabLife #PhDdays

Today the protein purification was a success. It took - loads of help from PostDoc, Doc El-Hadji - histidine tag cleavage expert, Stephane - protein pellet of PI, Marcin n six days of purif, which would otherwise take 2-3days. The thing I enjoyed the most? Autoclaving the medias :p Science is fun!

Our PI is this years' HFSP (The Human Frontier Science Program research) grant holder... Proud! www.inc.cnrs.fr/fr/cnrsinfo/...

Heartbreak....when the only protein complex you are confident about having a structure, especially after the crystals diffract beautifully, with good resolutions and space groups, does not show any structure, its a heartbreak. Its not the failures, its the expectations that hurt. #PhDlife

Tryptophan just gained recognition: as an open quantum system interacting with its environment and capable of carrying information million times faster than classical information processing. www.science.org/doi/10.1126/...

Also for those wondering about the first word of this post "another", the first filament work by our team was on ZBTB protein family which is and will remain our teams' first love headed by Lucija Mance and the brainchild of our PI,Marcin. Here is the link of the article www.cell.com/molecular-ce...

This website will make your neurons happy... Do have a look...

Another filament story from our team, this time on Ub E3 ligase, SIAH1. The entire analysis is hardwork of Franck, our cool collaborator Sebastien and Lucija's and mine PI, Marcin. The contribution of our team continues towards the realms of Science less traversed by. Just proud!

One of my crystal plate had this character today. Life is full of surprises 🌟

Days like these- -when one protein precipitates -another protein gellifies -wrong buffer is added to a protein crystal -ITC didn't work as planned And things don't work the only day you want them to work... #PhDdays

I've been hoping that someone would attempt to train a structure prediction model against experimental data (rather than 3D coordinates), and hopefully this is a step in that direction SFCalculator: connecting deep generative models and crystallography doi.org/10.1101/2025...

In this issue of Cell, Deng et al. provide a proteomics atlas for 1706 human diseases. The cover image portrays a human composed of proteins who is examining their health status (represented by the ECG monitoring interface) with the assistance of AI. Source: Cell, Volume 188, January 9, 2025

Color is the keyboard, the eyes are the harmonies, the soul is the piano with many strings. – Wassily Kandinsky

Karplus will remain a pioneer of MD simulations. Writing his first paper at the age of 17, n developing a significant force field- CHARMM, along with describing correlation b/w coupling constants and dihedral angles thru Karplus equation, spin coupling and a lot more, this man will remain a legend.

What's interesting here is - E4 ligase complex....diving into another world altogether! - structure elucidation of a megadalton complex! - and on top of that this E4 complex is conserved across eukaryotes! Science is literally Sciencing in this work. 👏 👏 👏