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Biohub releases a world model of protein biology

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Re: Biohub releases a world model of protein biology

#21

Post by cloche »

mettamage wrote: post #4
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…

Quite frankly, most people on HN are software devs with a wider interest in the world. HN’ers usually-ish comment when they have something insightful to sat, even if the insight is just a humble one. But I dare to guess that most HN’ers did high school bio and that’s it, so it’s harder to even give a small thoughtful comment on it, so they refrain. Case in point, I wouldn’t have commented either. But I feel at home h…

I think this is it. I'm a general software engineer and would like to switch to being in this field but something like this is just way over my head. It sounds like a great innovation but I'm lacking the domain knowledge to fully understand it. I've spent several months going through online courses to basically get to a Biology 101 understanding. Getting to the level of understanding something like this seems like it would be a multi-year effort and I don't really know what's the best way to proceed.

Re: Biohub releases a world model of protein biology

#22

Post by wombatpm »

rguiscard wrote: post #5

A similar work is Foundry ( https://github.com/RosettaCommons/foundry ). While both of them are good, the main issue is that it is not accurate enough at atom level. There are good chances that predicted or designed active site is slightly different from the real structure solved by X-ray, NMR or cryo-electronic microscopy. A side-chain or two may turn the other way so that it changes how the interaction is interpret…

But that is also a problem with structures derived from the methods you list. None of them are 100% equivalent to in vivi structures.

Re: Biohub releases a world model of protein biology

#23

Post by margalabargala »

bonsai_spool wrote: post #14
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…

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

Yes, because the expensive part is making the thing.

Re: Biohub releases a world model of protein biology

#24

Post by semiinfinitely »

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…

Biologists have a superiority complex about the “complexity” and “singular difficulty” of their field born out of a need for justification for the vast deficiencies of their field’s progress compared to others. Its an elaborate coping mechanism where the people in other fields which make envyable progress (eg software, cs etc)- sighted enough to have recognized and avoided the decrepitude of biological sciences- are in fact the ignorant ones who “struggle” , “incapable of grasping” the way that biologists think. Its an inversion designed to obscure the harsh truth that these outsiders in fact see quite clearly the way that biologists think and it is the reason they have so diligently avoided their field.

Re: Biohub releases a world model of protein biology

#25

Post by throwaway67678 »

semiinfinitely wrote: post #24
a_bonobo wrote: post #12

Earlier quoted context omitted.

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…

Biologists have a superiority complex about the “complexity” and “singular difficulty” of their field born out of a need for justification for the vast deficiencies of their field’s progress compared to others. Its an elaborate coping mechanism where the people in other fields which make envyable progress (eg software, cs etc)- sighted enough to have recognized and avoided the decrepitude of biological sciences- are…

The deficiencies of biology's progress as a field? The decrepitudes of biological sciences? Do we live in the same timeline?

Re: Biohub releases a world model of protein biology

#26

Post by ethanwillis »

semiinfinitely wrote: post #24
a_bonobo wrote: post #12

Earlier quoted context omitted.

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…

Biologists have a superiority complex about the “complexity” and “singular difficulty” of their field born out of a need for justification for the vast deficiencies of their field’s progress compared to others. Its an elaborate coping mechanism where the people in other fields which make envyable progress (eg software, cs etc)- sighted enough to have recognized and avoided the decrepitude of biological sciences- are…

You're simply wrong. I say this as a computer scientist who ended up studying and working in bioinformatics for a period of time.

The reason I don't now? It's that people don't understand biology enough to understand the currently untapped potential and definitely not the advances that have happened. So they allocate money to yet another todo app, food delivery app, crypto wallet, or yet another finetune of a model to talk like a caveman.

Re: Biohub releases a world model of protein biology

#27

Post by chromatin »

bonsai_spool wrote: post #14
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…

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

Yes because a core reason fro this technology is evaluation of de-novo designs (small peptide binders; scFvs; sdAbs)

Re: Biohub releases a world model of protein biology

#28

Post by ta988 »

RobotToaster wrote: post #10

> This model is released under the MIT License. Huh, appears to be actually open source, that's a pleasant surprise. Usually these academic models have some weird license attached to them.

Boltz (they likely have private ones with their company now), ESM are MIT licensed as well. Alphafold older versions were Apache. In this specific subfield, it looks like open is more common than not.

Re: Biohub releases a world model of protein biology

#29

Post by a_bonobo »

MrBuddyCasino wrote: post #19
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?

Oh no, that's just coincidence. In proteomics world, a peptide is just a short protein (<50 amino-acids?).

Re: Biohub releases a world model of protein biology

#30

Post by swyx »

zachthewf wrote: post #18
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

and it is a capital N nonprofit https://latent.space/p/biohub
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