Kate Stafford
@kastacholamine.bsky.social
AI/ML for proteins, small molecules, and everything in between. Scientist @AtomwiseInc. (she/her) 🌈 Previously: UCSF, Columbia, DE Shaw Research, MIT.
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.
March 4, 2025 at 12:56 AM
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.
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?
February 18, 2025 at 5:10 AM
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?
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”
Yes: “Free eggs from the Democrats”
No: “Amplifying the voices of marginalized communities by expanding access to traditional foodways impacted by capitalist climate injustice”
All these articles about Democrats moaning over their messaging issues make me tired.
You know what's more important than messaging? ACTION.
Don't TALK about the price of eggs.
Tell people "MEET US IN THE PARK - WE'RE GIVING OUT FREE EGGS. THAT'S RIGHT - FREE EGGS FROM THE DEMOCRATS!"
You know what's more important than messaging? ACTION.
Don't TALK about the price of eggs.
Tell people "MEET US IN THE PARK - WE'RE GIVING OUT FREE EGGS. THAT'S RIGHT - FREE EGGS FROM THE DEMOCRATS!"
February 16, 2025 at 12:37 AM
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”
Yes: “Free eggs from the Democrats”
No: “Amplifying the voices of marginalized communities by expanding access to traditional foodways impacted by capitalist climate injustice”
I get wanting to reduce government inefficiency, but starting with foreign aid and biomedical research is crazy. The TSA is right there!
February 9, 2025 at 5:25 PM
I get wanting to reduce government inefficiency, but starting with foreign aid and biomedical research is crazy. The TSA is right there!
Have to admit I was expecting the “find out” phase of Trump 2.0 to start later than week 2.
February 2, 2025 at 11:26 PM
Have to admit I was expecting the “find out” phase of Trump 2.0 to start later than week 2.
Reposted by Kate Stafford
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
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.
github.com
January 23, 2025 at 2:12 PM
Machine Learning in Drug Discovery Resources page updated for 2025. github.com/PatWalters/r...
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.
January 21, 2025 at 5:48 PM
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.
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.
January 20, 2025 at 3:40 AM
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.
Reposted by Kate Stafford
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...
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...
Classics in Medicinal Chemistry #1: Atorvastatin
Lipitor
medchemash.substack.com
January 17, 2025 at 11:46 PM
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...
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...
I accidentally put a cat toy in the washing machine and now the whole laundry pile smells like I used catnip-scented detergent.
January 13, 2025 at 6:32 AM
I accidentally put a cat toy in the washing machine and now the whole laundry pile smells like I used catnip-scented detergent.
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
Rewinding a cassette with a pencil
Blowing on a video game cartridge even though you kind of suspected it was just a placebo
what’s your favorite instance of haptic nostalgia—the poignant memory of the physicality of an obsolete thing—like dialing a rotary phone, shifting gears in a manual transmission, opening a soda can with a pull ring?
January 13, 2025 at 1:37 AM
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
Rewinding a cassette with a pencil
Blowing on a video game cartridge even though you kind of suspected it was just a placebo
Reposted by Kate Stafford
It's like Zuckerberg is doing a Buscemi "Hello fellow Trumpers" gif.
January 12, 2025 at 7:51 PM
It's like Zuckerberg is doing a Buscemi "Hello fellow Trumpers" gif.
He’s getting divorced isn’t he
Yep, the problem definitely is that we don’t have enough men in charge. 🫠🤬
www.bloomberg.com/news/article...
www.bloomberg.com/news/article...
Zuckerberg Says Most Companies Need More ‘Masculine Energy’
Mark Zuckerberg lamented the rise of “culturally neutered” companies that have sought to distance themselves from “masculine energy,” adding that it’s good if a culture “celebrates the aggression a bi...
www.bloomberg.com
January 12, 2025 at 8:27 PM
He’s getting divorced isn’t he
Fight! Fight! Fight!
I'll have to take Elon's side on this one, despite Bannon's doubtlessly sincere DEI concerns.
I'll have to take Elon's side on this one, despite Bannon's doubtlessly sincere DEI concerns.
January 12, 2025 at 5:15 AM
Fight! Fight! Fight!
I'll have to take Elon's side on this one, despite Bannon's doubtlessly sincere DEI concerns.
I'll have to take Elon's side on this one, despite Bannon's doubtlessly sincere DEI concerns.
Reposted by Kate Stafford
Reposted by Kate Stafford
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...
www.cell.com/cell/fulltex...
January 6, 2025 at 11:47 PM
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...
www.cell.com/cell/fulltex...
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.
January 4, 2025 at 10:58 PM
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.
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.
January 2, 2025 at 4:32 AM
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.
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….
December 29, 2024 at 9:05 PM
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….
Reposted by Kate Stafford
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
Happy holidays everyone!
www.plinder.sh/blog/updates
Updates
Updates
www.plinder.sh
December 24, 2024 at 3:56 PM
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
Happy holidays everyone!
www.plinder.sh/blog/updates
Good thing flight tracker sites exist so you can stress about how the plane assigned to your flight is late two legs before yours.
December 24, 2024 at 2:31 AM
Good thing flight tracker sites exist so you can stress about how the plane assigned to your flight is late two legs before yours.
Reposted by Kate Stafford
Just finding us here? Endpoints News has a starter pack with our journalists so you can follow the team!
go.bsky.app/NzDRUhL
go.bsky.app/NzDRUhL
December 17, 2024 at 7:38 PM
Just finding us here? Endpoints News has a starter pack with our journalists so you can follow the team!
go.bsky.app/NzDRUhL
go.bsky.app/NzDRUhL
Both cats are in my lap at the same time. That’s 24.5 pounds of cat. That is so much cat.
December 16, 2024 at 6:46 AM
Both cats are in my lap at the same time. That’s 24.5 pounds of cat. That is so much cat.
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.
December 15, 2024 at 4:29 PM
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.
Reposted by Kate Stafford
Protenix, the AF3 reproduction made by TikTok's parent company ByteDance, is now available for commercial use with an Apache 2.0 license
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.
github.com
December 13, 2024 at 4:48 PM
Protenix, the AF3 reproduction made by TikTok's parent company ByteDance, is now available for commercial use with an Apache 2.0 license