What a treat! What do you think is the future of Biophysics?

I think a lot about the man I was named after and how he performed both masculinity and ungendered public leadership. Victorian suppression of emotion is deeply dysfunctional as a *totalizing* concept but like, damn, some folks need to learn the value of a stiff upper lip in public.

The Moore-Penrose pseudoinverse is one of those things in linear algebra that everyone sort of knows about but fewer people than you would think actually Know about

Before knowing anything else about this, I am excited because prediction of stoichometry is also an implicit prediction of allostery.

Did I tell you all about the dynamical systems theorist that got caught gambling on the local tennis league I was a part of? She was fixing points.

This has been up for a while but I haven’t really publicized it. Introducing ciMIST: sparse, self-consistent network models of local and global protein conformational entropy, learned from molecular dynamics. This helps with analyzing MD and connecting to experiments www.biorxiv.org/content/10.1...

> paper claims astonishing progress on protein folding problem > ask if it’s interesting proteins or villin headpiece denatured with urea > they say results are robust to protein sequence properties > open the pdf > villin headpiece in urea

My most important scientific mentors and the scientists I most look up to are mostly women: Veronica Vaida, Jenny Glusker, Ann Skalka, Janet Thornton, Jane Richardson, Helen Berman. Happy International Women’s Day! @asbmb.bsky.social

sometimes when i put “best” at the end of an email i don’t really wish them my best

Two brothers from South Texas and their high school mariachi bandmates were recognized by their congresswoman last June for winning a state mariachi competition. Nine months later, the brothers, along with their parents and younger brother, are in ICE detention and facing deportation.

Did not expect this: "To illustrate this evolution, a phylogenetic tree constructed from the similarity of word content of abstracts shows a remarkably regular ‘ladder-like’ topology, with each successive year being most similar to its preceding year" from journals.biologists.com/bio/article/...

Out today: We discovered new viral proteins that target immune signaling molecules, solely based on their AlphaFold-predicted shapes www.science.org/doi/10.1126/... Congrats Nitzan Tal and coauthors! Thank you Kranzusch lab for the fun collaboration! Linking below previous thread on our findings

the web is a customer service medium, thats why its so unpleasant imo like trying to have a good time with the other people in line to return a defective vacuum and a yeti rambler to target

They will give Kaitlin computer 😈

It’s rumored that I am in NYC

Ayatollah Ali Khamenei, the supreme leader of Iran, was killed Saturday after the US and Israel launched airstrikes on Iran, according to President Donald Trump. He was 86.

So proud of this work with @rolanddunbrack.bsky.social! Did a lot of new structural bioinformatics of substrate-bound kinases and came up with updated criteria for classifying structures as active. Also made active models of all 437 human catalytic kinases, available here: dunbrack.fccc.edu/kincore

Great work from post-doctoral fellow @joanzone.bsky.social: New preprint on identifying active structures of protein kinases -- capable of binding ATP, Mg ions & especially substrates -- +modeling all 437 human catalytic protein kinase domains in their active conformation. doi.org/10.64898/202...

Broke: dead internet theory Woke: undead internet theory

I’m always saying this

hi guys I know I haven't been very active lately, and I don't talk about where I'm from often, but the government made some really scary announcements today so I thought I'd share to let everyone know what's happening. here are some posts from twt for context

Our paper is now out in Nature: “Ancient co-option of LTR retrotransposons as yeast centromeres” www.nature.com/articles/s41... A short thread on how retrotransposons helped give rise to yeast point centromeres. 1/14

I have yet to see anything more impressive than those side projects programmers used to show off on hackernews but maybe I’m not looking in the right places.

do I have any followers in Canada (Toronto, Ottawa, Montreal) who are academics and think they have anything academic overlap with what I do (complexity and predictive modeling, information theory)? I'm planning a Canada tour and am interested in hitting as many academic centers as possible

What’s the most impressive piece of AI-coded software you’ve seen? Bonus points for comp biophys

theres kind of a fun read of this to do where its about the cost of signifiers: a lot of peoples' wages went down in terms of F-250s

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

kresten is cooking this year

best halftime show ever

“im not familiar with bad bunny but..” i mourn for the lack of baddies in your life brother

At the jazz club with @justktln2.bsky.social . Claiming Your Mind Is On Vacation is by Taj Mahal. I put on the Buddy Guy version. I tell the youth about “his life”, clearly substituting Allen Toussaint’s biography. The real heads are gnashing their teeth. They don’t know that I have no fear of death

Starting to feel insane because of how often I’m seeing people train a generative model for protein conformational ensembles and then inspect with a tICA embedding. Why are people applying a time-dependent analysis to iid samples???

Notably, this is from Anthropic!

lol. Source: www.tiktok.com/t/ZP8HXPY8S/

incredible stonewalling by Wolfram's assistant here lmao, good show

I feel insanely lucky to have had my adolescence line up perfectly with the peak of music/film/art/aesthetics

Updating a 56 year-old JCB paper with digitized videos from 16 mm film 😍. Well done first author Tom Pollard!!

we love a global regulator of membrane signaling

wonder if this would see tech co market structure going the way of banks where failed firms are absorbed by more successful ones — ie at the right price does apple buy up microsoft as a distressed assets, support+transition systemically-important Microsoft products? does govt broker deal?

“I watched him die… then I watched them maneuver his body like a rag doll— only to discover it was because they wanted to count the bullet wounds and see how many they ‘got’, like he was a deer.”

Conroe ISD banned a book about Billie Jean King because it mentions her gay marriage: "'It is developmentally inappropriate to provide explicit explanations of sexual orientation and adult marital relationships to this age group' Conroe ISD Trustee Melissa Semmler said" www.chron.com/sports/artic...

Middlecamp says school attendance fell below 50%. Events are cancelled in a way likened to the COVID pandemic, she says.

CBP chief Bovino has confirmed that the officers who executed Alex Pretti in the street yesterday are not only *not on administrative leave,* they have all been reassigned to other jurisdictions and are all on the street today. This is totally unheard of for any officer-involved shooting

i havent shut off the notification for this form and it has just been vibrating every minute in my hand. just a steady beat.

Alex from our time working together, while he was in nursing school. Later, he moved to ICU, working as a nurse to support critically ill Veterans. He had such a great attitude. We’d chat between patients about trying to get in a mountain bike ride together. Will never happen now

One of my most peculiar pet peeves is when people temporally smooth molecular dynamics simulations before they make videos. To me it obscures the real wonder, which is that biological macromolecules do stuff so reliably even with all that thermal randomization.

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

In the 2010s, the Icelandic tv station Channel 2 accidentally added subtitles from a gritty crime drama to an episode of Teletubbies. I have translated some of the highlights