The joint entropy decomposes as S(X,Y) = S(X) + S(Y|X) so if S(Y|X) is constant over the set of environments you care about you can probably just ignore Y. Importantly this is true regardless of what X and Y are!

watched this on repeat losing my shit for two nights now

Love a paper with figures that make me ask questions like “When’s the last time I saw a hydrated binding pocket?” “When’s the last time I really *saw* a binding pocket?” “When’s the last time I really *saw* a *protein*?” “When’s the last time I really *saw* a PROTEIN, man?”

Delightful work here from @martinvoegele.bsky.social and collaborators. Wonder more broadly how much potential there is for free energy calculations to be used for structural inference (ie, loosely speaking, the correct structure should converge more quickly to the right free energy estimate)

as someone who lived in the circled area: it is the worst place in the entire world

oh but that's claude 3.ploob! have you tried claude dingus? have you tried globglob? have you tried paying $1333/month for strrop? you should be paying for strrop. you need at least 500 tokens of pogostick. Zaza comes out in 6 months you should switch to that. you should use zaza

hypocrisy is the only type of evil the "view from nowhere" can conceive of, because hypocrisy requires no set of values except the subject's own. this gives an actor with no values at all utter invulnerability to press criticism.

keep calm and trust in thermodynamics

Ok so the euphoria season 3 was definitely written largely by AI right?

how could I pick a favorite when they’re all so cool? stop shaming me

My own suspicion isn’t that social media is making people unhappy but that people post less when they’re happy. Waiting around in the dentist’s office is probably in the top decile of headspace people are in for posting. That biases towards negative sentiment overall, with economy as a special case

Need to create the Instagram Price Index. Annual 2 week Eurotrip, tasting menus weekly, bottle service once a month, DoorDash weekdays, useless kitchen gadgets, mid century modern furniture, millennial gray paint, weight loss peptides, Korean skincare products, the whole nine yards

Apply to work with some great people on one of the most exciting technologies in protein science!

A message for you all to carry through the year

Our review on ML for modeling conformational ensembles is out now in Current Opinion in Structural Biology (w/ @sonyahanson.bsky.social)! It's been exciting to follow all the progress in this field recently, and I'm equally excited to see where it goes! www.sciencedirect.com/science/arti...

Of course Dallas isn’t letting me out of here forever without _one last delayed flight_

Forgot how chatty Texans are

It’s like I’m stating into @justktln2.bsky.social ‘s soul

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