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Coronavirus Spike Protein Binder Design

fold.it

31–40 of 85 posts

Re: Coronavirus Spike Protein Binder Design

#31

There is already stuff like this out there: https://www.biorxiv.org/content/10.1101/2020.02.01.929976v2.... Also, it appears as though convalescence therapy is working (i.e., treating people with the plasma from recovered patients) https://www.straitstimes.com/asia/east-asia/china-seeks-plas... https://news.yahoo.com/chinese-doctors-using-plasma-therapy-...

Why cant they just extract the protein from the coronavirus?

Re: Coronavirus Spike Protein Binder Design

#32
post #2

I know it's fun, and I think participative science is such a huge shift in paradigm … But considering the global impact of coronavirus, I'm wondering if there shouldn't be a better way to fund this type of endeavor. Any cloud provider willing to donate compute to researchers?

The big cloud providers already donate a fair amount of compute (for example, some time ago I ran exacycle, which provided teams like FOlding@Home and Rosetta with extensive computing power. However, the economics of cloud are such that nearly all large-scale compute needs to provide revenue to the cloud provider for the provider to stay competitive. I've worked with the US gov't funding agencies in the past to make it possible to get "cloud credits" instead of grant $$$ (and even sat on panels that selected grants to promote cloud computing over closet clusters). The US works quite slow.

IIRC, fold.it is from David Baker, and he has a stable funding pipeline due to the sucess of Rosetta.

Re: Coronavirus Spike Protein Binder Design

#33
post #32
post #2

I know it's fun, and I think participative science is such a huge shift in paradigm … But considering the global impact of coronavirus, I'm wondering if there shouldn't be a better way to fund this type of endeavor. Any cloud provider willing to donate compute to researchers?

The big cloud providers already donate a fair amount of compute (for example, some time ago I ran exacycle, which provided teams like FOlding@Home and Rosetta with extensive computing power. However, the economics of cloud are such that nearly all large-scale compute needs to provide revenue to the cloud provider for the provider to stay competitive. I've worked with the US gov't funding agencies in the past to make…

Governments have a staggering amount of computational power. Good will is nice and all, but are we putting our tax payer funds to an obvious public need?

Re: Coronavirus Spike Protein Binder Design

#35
post #30

Earlier quoted context omitted.

I’m sorry to hear about your wife’s friend. But both examples you gave (people having to fight for further diagnoses of outside-case health problems) are really common with private healthcare in the United States too - we’ve just shifted the burden of cost of treatment/quality of life decisions to private entities who typically are only interested in furthering shareholder value. To give a personal anecdote as well:…

Agreed, the US system is flawed. I suppose with public-funded healthcare, everyone is on the same level - the survival rates of breast cancer and bowel cancer is the same for all (unless you can afford to fly to the US and pay for care there).

There can still be large variations across hospitals and doctors in a public system in terms of outcome.

Re: Coronavirus Spike Protein Binder Design

#36

There is already stuff like this out there: https://www.biorxiv.org/content/10.1101/2020.02.01.929976v2.... Also, it appears as though convalescence therapy is working (i.e., treating people with the plasma from recovered patients) https://www.straitstimes.com/asia/east-asia/china-seeks-plas... https://news.yahoo.com/chinese-doctors-using-plasma-therapy-...

Why cant they just extract the protein from the coronavirus?

I doubt it's easy to isolate

Re: Coronavirus Spike Protein Binder Design

#37
Strange site. The heading implies that they are attempting to design things that help science, but if you drill in to the pages for "new to fold.it" and FAQ, it never actually says that any of the results are used by anyone. Instead it says that it's all a game and the only science goal is to prove that humans are capable (just like computers) of doing this.

I wonder if this is really all it is, or if the writers of the FAQ are just myopic about the fact that newcomers don't have the big picture, so they just forget to mention whether the results are ever used or not, or even potentially used, or even potentially looked at by anyone who might use them.

Reminds me of how a lot of open source packages, when you go to their about page, just have a list of recent updates in highly technical language that assumes the reader is already familiar with the goals of the project.

Sites should not assume that the reader already knows what is going on. In this case, the "new to fold.it" page is just a bunch of steps for getting started, with absolutely no overview that makes clear how any of it is all used. Under "goals" the stated science goal is just to prove that humans can solve this kind of puzzles. Really odd that teams would give time to this if it's not having any real effect though, so I suspect I'm missing something?

Re: Coronavirus Spike Protein Binder Design

#39
post #37

Strange site. The heading implies that they are attempting to design things that help science, but if you drill in to the pages for "new to fold.it" and FAQ, it never actually says that any of the results are used by anyone. Instead it says that it's all a game and the only science goal is to prove that humans are capable (just like computers) of doing this. I wonder if this is really all it is, or if the writers of…

I happened to work in the lab at the University of Washington that helped maintain the game as an undergrad. Here's a published scientific article about the use of Foldit for science: https://www.nature.com/articles/nature09304

(I'm not disagreeing that the website is badly designed.)

Re: Coronavirus Spike Protein Binder Design

#40
post #13
post #7

Earlier quoted context omitted.

Isn't blood pretty good at this?

I'm not a biologist but I suppose that not every kind of protein enters any kind of cell.

You need these proteins to interfere with viruses before they enter cells, so that part is probably fine.
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