Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

Biohub releases a world model of protein biology

biohub.org

Post reply on HN
Print view View original

11–20 of 33 posts

Re: Biohub releases a world model of protein biology

#11

Post by a_bonobo »

The accompanying preprint is interesting: https://www.biorxiv.org/content/10.64898/2026.06.03.729735v1

Modeling protein-protein binding is still a massively unsolved problem, mainly because we don't really have the data. Alphafold2 was great but didn't actually 'solve' protein-folding as all input data is from single 'state' X-ray crystallography of the proteins, not 'really' how these proteins behave in the wild. So it's still very, very had to predict what binds to what, which of course is a multi-billion-dollar industry.

I work in a pharma-field and I wish we could easily design molecular binders. We still spend millions every year finding targets that could 'smuggle' our drugs into cells.

Some other players in this field are Boltz Lab and Isomorphic Labs (the Alphafold Google spinoff led by Hasabi). None of them can predict anything complex or 'big', everything is peptide-level. OP's work is another step towards something better.

The most interesting part in the preprint is that they find no matches for their designed binders in the world-write protein database. An open question with protein-designers is whether they just regurgitate training material, which is far easier to test with English-language models.

Re: Biohub releases a world model of protein biology

#12

Post by a_bonobo »

ethanwillis wrote: post #7
Frannky wrote: post #3

It's interesting that there are almost no comments on this. This feels like some of the most exciting and impactful fields of the next years. I worked with a cracked researcher that was generating molecules a couple of years ago. She spent most of her time fighting cuda bugs and trying installing packages. I wonder if the ecosystem matured right now. There are people studying cells to see what enters and what exits a…

I'm sure people will take this the wrong way, but a lot of the people who are on HN and who orbit technology circles in SF are really just not actually intellectually curious people. They might like to think they are, they might try to pretend they are, but when pushed they're simply not. Look at all of the groupthink that is perpetuated nonstop while they also proclaim they're creating, investing in, etc. so many un…

I'd go even further: what happens in biology is antithetical to the way software people think.

The HN/YC crowd generally has software brain: https://www.theverge.com/podcast/917029/software-brain-ai-ba..., "when you see the whole world as a series of databases that can be controlled with the structured language of software code". Biology doesn't work like that most of the time, it's squishy and weird and unpredictable, and the models we have of biology (including genomics!) are faulty at best, misleading at worst. I've supervised PhD-students and it takes some time for people's brains to be comfortable with that squishiness, that random behaviour, that 'putting A into the system only rarely produces B and we don't really know why but we do it anyway' view of the world. Software engineers struggle, even abhor that kind of world, which is why you rarely see them being interested in it; and if they work in it, outcomes are sometimes amazing and Nobel Prize worthy, more often nonsense that silently disappears.

Re: Biohub releases a world model of protein biology

#13

Post by trilogic »

It is a nice work, however the domain specific finetuning will always be of higher accuracy prediction. Another thing worth noting is the sequence length used for the training (usually cut to 1024/2048) which is a game changer if left uncut.

I did have a bit of fun myself finetuning esm2 in domain specific bacteria (cause it gives better score) and comparing it to another model (self created) and self created beat it at 25% more accuracy. Then for the 3d structure was coded a 3d protein visualizer hypergraph with the upload file option and visualize instantly the result. 2 days job :)

Re: Biohub releases a world model of protein biology

#14

Post by bonsai_spool »

a_bonobo wrote: post #11

The accompanying preprint is interesting: https://www.biorxiv.org/content/10.64898/2026.06.03.729735v1 Modeling protein-protein binding is still a massively unsolved problem, mainly because we don't really have the data. Alphafold2 was great but didn't actually 'solve' protein-folding as all input data is from single 'state' X-ray crystallography of the proteins, not 'really' how these proteins behave in the wild. So…

> very had to predict what binds to what, which of course is a multi-billion-dollar industry.

Do you need to predict when AP-MS is so cheap?

Mapping interaction interfaces is challenging and is where there is attention. I don’t think we’re going to get complexes as a commercial focus outside of receptors with known quaternary structure. The first issue, as you allude to, is the absence of training data, which itself highlights the relative commercial unimportance of such an endeavor.

Re: Biohub releases a world model of protein biology

#15

Post by swasheck »

a_bonobo wrote: post #12
ethanwillis wrote: post #7

Earlier quoted context omitted.

I'm sure people will take this the wrong way, but a lot of the people who are on HN and who orbit technology circles in SF are really just not actually intellectually curious people. They might like to think they are, they might try to pretend they are, but when pushed they're simply not. Look at all of the groupthink that is perpetuated nonstop while they also proclaim they're creating, investing in, etc. so many un…

I'd go even further: what happens in biology is antithetical to the way software people think. The HN/YC crowd generally has software brain: https://www.theverge.com/podcast/917029/software-brain-ai-ba... , "when you see the whole world as a series of databases that can be controlled with the structured language of software code". Biology doesn't work like that most of the time, it's squishy and weird and unpredictab…

> Biology doesn't work like that most of the time, it's squishy and weird and unpredictable, and the models we have of biology (including genomics!) are faulty at best, misleading at worst.

interesting. i came to tech from a molecular biology background and my impression was the opposite. biology is predictable most of the time, but sometimes random and squishy. the trick is that we’re trying to learn why things work predictably and what causes the variations, and that why/how unknown is what is most uncomfortable for people outside of the disciplines.

i’m not fully disagreeing with you because it sounds like you have experiences that inform your perspective. i find it interesting because my own experiences bring me in from the inverse perspective.

Re: Biohub releases a world model of protein biology

#16

Post by Gooblebrai »

a_bonobo wrote: post #12
ethanwillis wrote: post #7

Earlier quoted context omitted.

I'm sure people will take this the wrong way, but a lot of the people who are on HN and who orbit technology circles in SF are really just not actually intellectually curious people. They might like to think they are, they might try to pretend they are, but when pushed they're simply not. Look at all of the groupthink that is perpetuated nonstop while they also proclaim they're creating, investing in, etc. so many un…

I'd go even further: what happens in biology is antithetical to the way software people think. The HN/YC crowd generally has software brain: https://www.theverge.com/podcast/917029/software-brain-ai-ba... , "when you see the whole world as a series of databases that can be controlled with the structured language of software code". Biology doesn't work like that most of the time, it's squishy and weird and unpredictab…

The world of uncertainty and the idea that we might not be able to understand everything or control it as much as we'd like.

It seems to me a lot of the modern "tech-bro culture" is trying to control the future and reduce uncertainty: Stop death, merge with the robotic super intelligence, colonize Mars to escape Earth inevitable decay, etc.

I'm still waiting for the startups claiming to reduce entropy or solve the false vacuum decay

Re: Biohub releases a world model of protein biology

#17

Post by marcuskane2 »

Frannky wrote: post #3

It's interesting that there are almost no comments on this. This feels like some of the most exciting and impactful fields of the next years. I worked with a cracked researcher that was generating molecules a couple of years ago. She spent most of her time fighting cuda bugs and trying installing packages. I wonder if the ecosystem matured right now. There are people studying cells to see what enters and what exits a…

This was posted on a Saturday night (in the US). A story posted at lunch time on a Tuesday is going to get 100x or maybe 10,000x more views than a story posted on a Saturday night.

It's not that HN readers lack intellectual curiosity or have some character flaw or narrow worldview, it's just that few people are reading and commenting between the late hours of Saturday and early morning of Sunday. It's 6 am Sunday in California as I post this.

Re: Biohub releases a world model of protein biology

#18

Post by zachthewf »

tmoertel wrote: post #9

Our mission is to cure or prevent all disease Okay, now you have my attention. What's the deal on the company behind it? “Biohub is a 501(c)(3) biomedical research organization...” Nonprofit. Nifty! This all sounds great, but as we have recently seen with, say OpenAI, there is nonprofit and then there is nonprofit . Anyone know which Biohub is?

Biohub is funded by Zuck and his wife - the full name is "Chan Zuckerberg Biohub"

https://en.wikipedia.org/wiki/Chan_Zuckerberg_Biohub

Re: Biohub releases a world model of protein biology

#19

Post by MrBuddyCasino »

a_bonobo wrote: post #11

The accompanying preprint is interesting: https://www.biorxiv.org/content/10.64898/2026.06.03.729735v1 Modeling protein-protein binding is still a massively unsolved problem, mainly because we don't really have the data. Alphafold2 was great but didn't actually 'solve' protein-folding as all input data is from single 'state' X-ray crystallography of the proteins, not 'really' how these proteins behave in the wild. So…

> None of them can predict anything complex or 'big', everything is peptide-level.

Is this related to the current peptide boom?

Re: Biohub releases a world model of protein biology

#20

Post by SubiculumCode »

a_bonobo wrote: post #12
ethanwillis wrote: post #7

Earlier quoted context omitted.

I'm sure people will take this the wrong way, but a lot of the people who are on HN and who orbit technology circles in SF are really just not actually intellectually curious people. They might like to think they are, they might try to pretend they are, but when pushed they're simply not. Look at all of the groupthink that is perpetuated nonstop while they also proclaim they're creating, investing in, etc. so many un…

I'd go even further: what happens in biology is antithetical to the way software people think. The HN/YC crowd generally has software brain: https://www.theverge.com/podcast/917029/software-brain-ai-ba... , "when you see the whole world as a series of databases that can be controlled with the structured language of software code". Biology doesn't work like that most of the time, it's squishy and weird and unpredictab…

No biologist stays an essentialist for long, that is for sure.
Post reply on HN