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AlphaFold Protein Structure Database

alphafold.ebi.ac.uk

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Re: AlphaFold Protein Structure Database

#41

Post by moistly »

narrator wrote: post #22

Gain of function researchers working for the world's militaries will use this research to figure out how to get viruses to attach to receptor sites peculiar to particular races. The people developing the antivirals will have a lot harder time countering these weapons because making antivirals that aren't poisonous in some weird way is a much harder job. If this is not the case, please let me know why, it will really…

> Ridiculous fookin’ idjit and compulsive liar M.T.Greene came out of a classified briefing recently and announced that the CCP is hard at work on race specific bioweapons.

Fixed that for you. By the way, you shouldn’t pay attention to that clown.

Re: AlphaFold Protein Structure Database

#42

Post by ricksunny »

tazjin wrote: post #9
ricksunny wrote: post #6

I’m sorry but why don’t tbey just release the ability for a user to enter a known real-world sequence’s accession number from Genbank / GISAID, and generate the protein structure from that? Why do they have to abstract the user from the process by only exposing a completed database of the protein structures the Alphafold researchers decided would be worth producing?

You can use the open-source code, and we also have a Colab notebook for that: https://bit.ly/alphafoldcolab More info: https://deepmind.com/blog/article/putting-the-power-of-alpha...

Thanks for that - I can see why my comment was downvoted now, as the the posted article's FAQ lists these links for those who would like to study their favorite sequenced-but-unmodeled protein. I'm glad Alphafold is as open source as it is, and I recognize that it didn't have to be so.

I think I was primed for a knee-jerk reaction because when Alphafold's results were announced back in Dec. 2020, with expressions of what a boon it would be for researchers around the globe, I anticipated there would be a timeline announced for exposing a tool or for the open-sourcing. (The Github repo has only just been released about 6 days ago ...)

With all the work on SARS-CoV-2's 'interactome', as well as human proteins & enzymes involved in pharmacology of antiviral drugs under development / repurposing , it's easy to imagine that drug developers would have liked to exercise Alphafold as soon as it was announced. (I myself have wanted a structure for human enzyme OATP1A2 that wasn't available on the PDB for such a drug pharmacology study - quite glad it is available at hand now.. .:) ).

Anyway I'm sure good arguments will be made about the need to really 'get it right' before releasing, or internal deliberations on how much to open up vs charging for it.

But 7 months lead time during a pandemic is a long time...

In all cases thanks again for this innovation's availability now. :)

Re: AlphaFold Protein Structure Database

#43

Post by narrator »

ravila4 wrote: post #39
narrator wrote: post #22

Gain of function researchers working for the world's militaries will use this research to figure out how to get viruses to attach to receptor sites peculiar to particular races. The people developing the antivirals will have a lot harder time countering these weapons because making antivirals that aren't poisonous in some weird way is a much harder job. If this is not the case, please let me know why, it will really…

1. Gain of function is not as easy as you think. 2. Such bio-weapons are not likely because any virus released in the wild will mutate over time, and also because you cannot target "races" in the way you describe. Phenotypic traits span across geographical borders, and any attempt to do such a thing is likely to backfire.

I think if the CCP were successful in creating race targeted bioweapons it would be in their interest to convince the world that they didn't exist.

Insults, character assassination campaigns and politicizing the existence of these bioweapons would be a good way to do that. Just copy paste some of the comments here and change the name to insult anyone who thinks they exist. They could then go and kill millions and not receive any retaliation whatsoever with people praising them for their effective program of keeping the disease epidemic they created under control. Even if you got the guy who discovered AIDS and won the Nobel prize for it to say that these were gain of function viruses that incorporated HIV protein parts, you could just launch a big propaganda campaign to attack his character.[1] Much cheaper than having to fight a war.

[1]https://www.gmanetwork.com/news/scitech/science/736458/frenc...

Re: AlphaFold Protein Structure Database

#44

Post by mlyle »

narrator wrote: post #31
narrator wrote: post #27

Earlier quoted context omitted.

I'm thinking that the problem is is that it is much harder to develop drugs that only kill cancers very efficiently and don't harm the rest of the body than to tweak viruses that just have to keep the person alive long enough to spread the virus.

The crazy part is a bioweapons program is really cheap compared to a nuclear weapons program, and now with these new tools it's even cheaper. Before, it was vastly more expensive to do the cycle of creating a new viral protein and testing a bioweapon on human cell culture. Now that process is speeded up millions of times with this technology because that can all take place inside a computer. This is similar to the ch…

Is this a correct summary of your statements:

Because it -might- make things slightly easier for a state actor with nigh-unlimited resources to enact a doomsday scenario, which they might or might not be pursuing, medical researchers should not publish otherwise helpful research?

Re: AlphaFold Protein Structure Database

#45

Post by ricksunny »

sveme wrote: post #8
ricksunny wrote: post #6

I’m sorry but why don’t tbey just release the ability for a user to enter a known real-world sequence’s accession number from Genbank / GISAID, and generate the protein structure from that? Why do they have to abstract the user from the process by only exposing a completed database of the protein structures the Alphafold researchers decided would be worth producing?

I'd guess the ad-hoc simulation of the structure is computationally quite expensive and takes a while, though that's just a guess and I haven't read the original paper yet.

In fact a cost of $1-$4 for the preferred implementation:

https://news.ycombinator.com/item?id=27894060

The colab provides a slightly-less-accurate version that operates in the cloud. For the real mccoy it seems one must set up one’s own environment and leverage the git repo.

Re: AlphaFold Protein Structure Database

#46

Post by narrator »

mlyle wrote: post #44
narrator wrote: post #31

Earlier quoted context omitted.

The crazy part is a bioweapons program is really cheap compared to a nuclear weapons program, and now with these new tools it's even cheaper. Before, it was vastly more expensive to do the cycle of creating a new viral protein and testing a bioweapon on human cell culture. Now that process is speeded up millions of times with this technology because that can all take place inside a computer. This is similar to the ch…

Is this a correct summary of your statements: Because it -might- make things slightly easier for a state actor with nigh-unlimited resources to enact a doomsday scenario, which they might or might not be pursuing, medical researchers should not publish otherwise helpful research?

I think it's great that the Wuhan institute published all their gain of function research. They even said who paid for it. It's a clear trail back to them, but apparently taking any action to acknowledge that this is a bad thing and something fishy might be going on is a completely politicized issue now that apparently gets as many downvotes as arguing about hot button political topics now.

What I'm saying is there should at least be an open and frank discussion of what the whole world is getting itself into right now with all this.

Re: AlphaFold Protein Structure Database

#47

Post by pelorat »

Ovah wrote: post #21

Interesting that they're porting it to other organisms. Different organisms have variations in ribosomes, post translational modifications and even tRNA repertoire. So it's not a guarantee that two identical DNA sequences will give identical proteins in two different organisms.

Shouldn't matter? Protein folding is based on the laws of physics after all. If DNA sequences folds differently in different organisms then an external factor is missing.
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