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Kate Stafford

@kastacholamine.bsky.social
3.3K followers 776 following 64 posts

AI/ML for proteins, small molecules, and everything in between. Scientist @AtomwiseInc. (she/her) 🌈 Previously: UCSF, Columbia, DE Shaw Research, MIT.

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Kate Stafford @kastacholamine.bsky.social · 04/03/2025
Every so often I google something and the top hits are Reddit threads from 10-15 years ago - which doesn’t seem that long ago, but everything about the slang and typing style and general vibe feels like falling into a time warp.
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Kate Stafford @kastacholamine.bsky.social · 18/02/2025
Am I the only one who always feels like I have to praise the LLM whenever it does a good job? Who's a good boy? Is Claude a good boy?
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Kate Stafford @kastacholamine.bsky.social · 16/02/2025
This! And at the risk of going back to the messaging issue… resist the temptation to speak nonprofitese about it. Yes: “Free eggs from the Democrats” No: “Amplifying the voices of marginalized communities by expanding access to traditional foodways impacted by capitalist climate injustice”
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Kate Stafford @kastacholamine.bsky.social · 09/02/2025
I get wanting to reduce government inefficiency, but starting with foreign aid and biomedical research is crazy. The TSA is right there!
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Kate Stafford @kastacholamine.bsky.social · 02/02/2025
Have to admit I was expecting the “find out” phase of Trump 2.0 to start later than week 2.
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Pat Walters @wpwalters.bsky.social · 23/01/2025
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
github.com
GitHub - PatWalters/resources_2025: Machine Learning in Drug Discovery Resources 2024
Machine Learning in Drug Discovery Resources 2024. Contribute to PatWalters/resources_2025 development by creating an account on GitHub.
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Kate Stafford @kastacholamine.bsky.social · 21/01/2025
I spent a long time building a dataset, finally started training a model on it, and was so relieved to see the loss go down. Maybe the data sucks, maybe the model will suck, but at least I didn’t scramble the labels or make unusable data mud.
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Kate Stafford @kastacholamine.bsky.social · 20/01/2025
If the worst thing that happens in Trump admin 2.0 is that he's super corrupt and scams some crypto bros, we will be getting off easy. In fact we should encourage him to spend as much of his time as possible on crypto.
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Ash Jogalekar @ashjogalekar.bsky.social · 17/01/2025
I have a new blog devoted to medicinal chemistry in which I will mainly focus on classic papers. My first installment describes the design and discovery of the amazing atorvastatin: a triumph of simple modeling, dogged synthesis and leadership decisions medchemash.substack.com/p/classics-i...
medchemash.substack.com
Classics in Medicinal Chemistry #1: Atorvastatin
Lipitor
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Kate Stafford @kastacholamine.bsky.social · 13/01/2025
I accidentally put a cat toy in the washing machine and now the whole laundry pile smells like I used catnip-scented detergent.
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Kate Stafford @kastacholamine.bsky.social · 13/01/2025
Going to a musty basement and turning those big cranks to move the stacks in the library Rewinding a cassette with a pencil Blowing on a video game cartridge even though you kind of suspected it was just a placebo
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David Darmofal @daviddarmofal.bsky.social · 12/01/2025
It's like Zuckerberg is doing a Buscemi "Hello fellow Trumpers" gif.
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Kate Stafford @kastacholamine.bsky.social · 12/01/2025
He’s getting divorced isn’t he
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Kate Stafford @kastacholamine.bsky.social · 12/01/2025
Fight! Fight! Fight! I'll have to take Elon's side on this one, despite Bannon's doubtlessly sincere DEI concerns.
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John Parkhill @johnparkhill.bsky.social · 10/01/2025
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Willow Coyote-Maestas @willowcoyote.bsky.social · 06/01/2025
Check out our work, where we discover how receptor GPCR senses pH! We solved a longstanding question by developing foundational GPCR DMS tech dev + structural bio! Led by brilliant PhD student @matthewkhoward.bsky.social and Nick Hoppe w/ @amanglik.bsky.social! www.cell.com/cell/fulltex...
cell.com
Molecular basis of proton sensing by G protein-coupled receptors
Howard et al. combine mechanistic deep mutational scanning, cryo-EM, and constant-pH molecular dynamics simulations to provide a holistic view of proton activation in human pH-sensitive GPCRs.
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Kate Stafford @kastacholamine.bsky.social · 04/01/2025
Maybe the problems I give them are too easy, but whenever I ask an LLM to generate some code, the results are fine. No need for super elaborate custom prompts or a ton of back and forth.
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Kate Stafford @kastacholamine.bsky.social · 02/01/2025
I’m happy to see more outdoor markets in SF, but come on. If the hours are 3-7pm it is not a “night market”, even in Noe Valley.
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Kate Stafford @kastacholamine.bsky.social · 29/12/2024
Went to a yoga class slightly hungry. By the end I spent the entire shavasana thinking about the burrito I was going to get after class. Mmm, burrito meditation….
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Janani Durairaj (Jay) @ninjani.bsky.social · 24/12/2024
Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving. Happy holidays everyone! www.plinder.sh/blog/updates
plinder.sh
Updates
Updates
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Kate Stafford @kastacholamine.bsky.social · 24/12/2024
Good thing flight tracker sites exist so you can stress about how the plane assigned to your flight is late two legs before yours.
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Endpoints News @endpts.com · 17/12/2024
Just finding us here? Endpoints News has a starter pack with our journalists so you can follow the team! go.bsky.app/NzDRUhL
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Kate Stafford @kastacholamine.bsky.social · 16/12/2024
Both cats are in my lap at the same time. That’s 24.5 pounds of cat. That is so much cat.
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Kate Stafford @kastacholamine.bsky.social · 15/12/2024
Do any of the big LLMs do gift subscriptions? Seems like OpenAI is a no. I hope at least one of these companies thought of this before Christmas.
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Diego del Alamo @delalamo.xyz · 13/12/2024
Protenix, the AF3 reproduction made by TikTok's parent company ByteDance, is now available for commercial use with an Apache 2.0 license
github.com
GitHub - bytedance/Protenix: A trainable PyTorch reproduction of AlphaFold 3.
A trainable PyTorch reproduction of AlphaFold 3. Contribute to bytedance/Protenix development by creating an account on GitHub.
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Kate Stafford @kastacholamine.bsky.social · 11/12/2024
I updated from a super old android phone to a new iPhone and I’m perversely fascinated by how the mix of ads I get has completely changed. Apparently I’m a much higher value customer now, and also willing to pay more for stuff.
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Kate Stafford @kastacholamine.bsky.social · 08/12/2024
Everyone in the anti-aging/lifespan extension space talks about the value of sleep and advises getting more. As much as I enjoy sleeping, reducing sleep needs would get you so much more actual life in your existing lifespan.
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Kate Stafford @kastacholamine.bsky.social · 07/12/2024
Somewhere there's a bunch of silicon-based life forms talking about how carbon-based meatware is fine for eating and reproducing, but a few pounds of low-energy jello is inherently incapable of reasoning and can't possibly scale enough for consciousness no matter how interconnected it gets.
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Kate Stafford @kastacholamine.bsky.social · 06/12/2024
Spicy! Good points on benchmarks and splits. When I read it I thought, if you're going to be that spicy you need a figure 8 showing how "competently run" docking does on the hard set from figure 7.
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Kate Stafford @kastacholamine.bsky.social · 04/12/2024
I just tried this and it worked the first time with no setup fuss or dependency annoyances or anything, just did exactly what the docs said it would do. That's so rare I have to celebrate it!
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 03/12/2024
Three BioML starter packs now! Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc Pack 3: go.bsky.app/NAKYUok DM if you want to be included (or nominate people who should be!)
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Kate Stafford @kastacholamine.bsky.social · 02/12/2024
Is apple intelligence good? I never hear anyone talk about it other than to post funny mistakes in summarizing someone's texts
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Brian Naughton @btnaughton.bsky.social · 30/11/2024
New blogpost: The ABCs of Alphafold 3, Boltz and Chai-1 blog.booleanbiotech.com/alphafold3-b...
blog.booleanbiotech.com
Boolean Biotech
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Olexandr Isayev 🇺🇦 🇺🇸 @olexandr.bsky.social · 30/11/2024
Proudly over one year (!!) under review. @chemrxiv.bsky.social preprint: "AIMNet2: A Neural Network Potential to Meet your Neutral, Charged, Organic, and Elemental-Organic Needs". Loooong time in the works...so excited to share this with #compchem #chemsky chemrxiv.org/engage/chemr...
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Kate Stafford @kastacholamine.bsky.social · 29/11/2024
It's a little3 hard to disagree with people who say the vibe is off around here when there's a parade of posts being performatively shocked that someone downloaded some public data from this website and put it on a different website.
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Kate Stafford @kastacholamine.bsky.social · 29/11/2024
My worst Thanksgiving take: I don't really like either pumpkin or pecan pie. Apple is the clearly superior fall pie.
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Kate Stafford @kastacholamine.bsky.social · 27/11/2024
I actually kind of like the look of the cybertruck (yes, I'm aware I have terrible taste) but seeing them try to do normal car things is so goofy. I'm watching one attempt to parallel park right now and doing my best to pretend I'm laughing at something on my phone and not this guy's parking job.
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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 27/11/2024
This should go chiral
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Kate Stafford @kastacholamine.bsky.social · 26/11/2024
One thing I think I missed about the whole Cassava story is why they had so many very online superfans. People inside getting mad about negative stories, OK, but most biotechs don't really have a fan club?
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)
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Kate Stafford @kastacholamine.bsky.social · 25/11/2024
That cofactor deserves it.
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YC Lin @yiechanglin.bsky.social · 19/11/2024
I made a MD starter pack! Dm or reply to be added ☺️☺️ go.bsky.app/QQjPjbL
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Kate Stafford @kastacholamine.bsky.social · 25/11/2024
I liked grad school! What made it work: 1) Liked where I lived. Hard to beat spending your 20s in NYC 2) Had a well-paid real job first: time to figure out post-college adulting and save some money 3) Chose a program with minimal requirements (classes, TAing) 4) PI, lab, and project were great
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Kate Stafford @kastacholamine.bsky.social · 24/11/2024
I am not a synthetic chemist and I am SO bad at this
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Kate Stafford @kastacholamine.bsky.social · 24/11/2024
This is a good point. I've gotten into the habit of using twitter likes as bookmarks for things to read later, but maybe other people have similar bookmark tastes. On the other hand I don't like to follow people who retweet constantly and rarely contribute anything original.
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Kate Stafford @kastacholamine.bsky.social · 23/11/2024
A lot of the posts on bluesky are still posts *about* bluesky. Needs to get less meta if this is going to take off. Yes, I know I'm contributing to the problem!
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Kate Stafford @kastacholamine.bsky.social · 21/11/2024
I hate cofactors. Are you part of the receptor or are you a ligand? Make up your mind!
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Kate Stafford @kastacholamine.bsky.social · 20/11/2024
Starting to think this app needs a starter packs starter pack. Some good ones (COI: I am in them, so they must be good) AI in science: go.bsky.app/JeFdryY Drug development: go.bsky.app/B2pzQm2 Women in chem: go.bsky.app/LjumNEg
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Kate Stafford @kastacholamine.bsky.social · 18/11/2024
What do you call posting on this website, I'm not sure I can unironically say "skeets"
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