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versailles
Community Member

Your PC vs COVID-19

I'm gonna to start this separate thread about this topic to avoid derailing the Coronavirus thread

 

Got a PC? A Mac? A server in a datacenter? Well, you can help fighting this Coronavirus! Biologists can fight diseases using computing power to run mathematical modeling of the rearrangement of proteins in viruses (folding) in order to find how to disable them. This requires some huge computational power.

 

Folding@Home is a biology research platform led by the computational biophysicist Greg Bowman, PhD, an associate professor of biochemistry and molecular biophysics at the Washington University School of Medicine in St. Louis, USA. Volunteers across the world can lend computing power of their home and work computers to the project, just by installing a software that will run in the background, for instance when the computer is idle.

 

Volunteers' computers are assigned Work Units, fragments of algorithmic calculations that they will process and send back once done.

 

Put together, the whole network of computers running Folding@Home is now the most powerful supercomputer in the world!

 

The project is used to do research about a whole host of diseases, but since March 2020 it is near to exclusively focused on COVID-19.

 

The COVID19 project: https://foldingathome.org/covid19/ 

 

On the University's website: Crowdsourced supercomputing project sets sights on coronavirus 

 

Get started now: Start folding 

 

 

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"Where darkness shines like dazzling light"   —William Ashbless
18 REPLIES 18
petra_r
Community Member

Brilliant. Just downloaded it!

gilbert-phyllis
Community Member

Brilliant. Fired up my desktop PC this morning to do this, only to discover I haven't used it since last summer and missed several Windows updates. It's been trying to catch up all day. (It exists primarily as a talisman to keep my laptop from dying in the middle of a time-sensitive project.)

 

I already posted this in the Covid thread, but it actually belongs here. This is the last win from the Folding@Home COVID-19 project (to which you can participate) as of April 3rd:

 

https://twitter.com/drGregBowman/status/1246106316864708608

 

CAPTURING THE COVID-19 DEMOGORGON (AKA SPIKE) IN ACTION
April 3, 2020
by Greg Bowman

The spike of the SARS-CoV-2 virus (shown below) is one particularly appealing target for designing therapeutics to combat the COVID-19 disease. It is actually comprised of three identical proteins arranged in a circle. Many copies of the spike protrude from the surface of the virus, where they wait to encounter a protein on the surface of many human cells, called ACE2. Binding of a spike to ACE2 initiates a series of events that ultimately allow the virus to enter the human cell. Therefore, therapeutics that bind the spike in a manner that blocks its interaction with ACE2 could provide a valuable means to prevent infection.

 

While extremely valuable, the structure shown above is far from a complete picture of how the spike works, or the ways that we could target it with therapeutics.

In fact, it is well-established that the spike must undergo a dramatic opening motion to reveal the interface that ultimately binds a human cell. Specifically, the spike has three receptor-binding domains that directly bind to ACE2 (the protein on the surface of human cells). For the spike-ACE2 interaction to form, the spike’s three receptor-binding domains must open up to reveal the binding interface.

The opening of the three receptor-binding domains reminded us of the mouth of the Demogorgon monster from the television series Stranger Things, so we’ve taken to calling the spike the COVID-19 Demogorgon.

Understanding how the spike opens up to engage the ACE2 protein could be extremely useful. Every step along the way could potentially be targeted with therapeutics.

Unfortunately, there is no way to watch a spike undergo this transition, at least with existing experimental techniques. Data on what the open state even looks like is also limited.

To overcome this limitation, we are using computer simulations to watch the COVID-19 Demogorgon open its mouth. To do this, we are using a two-stage process. In the first stage, we use an algorithm called FAST adaptive sampling that allows us to focus simulations on capturing specific structural changes, like the opening of the spike. While we can see these processes, it’s often still hard to say how long each stage of the process takes. Such information is valuable because long-lived steps are generally better therapeutic targets. To get that information, we then take representative structures from different stages of the opening process and start thousands of simulations on the Folding@home distributed computing platform. These simulations let us identify additional structures of the protein, determine the relative lifetimes of all the different structures, and prioritize them for drug development.

Both steps are extremely computationally expensive. If you tried to simulate the opening of the spike on your home computer, you’d be lucky to see even part of the process within the next 100 years. Even with the reasonably powerful computer cluster we run at the Washington University School of Medicine, we’d be hard put to capture this event. Needless to say, none of us wants to wait that long for a COVID-19 treatment to be developed.

Fortunately, we have reinforcements! Over the past three weeks, over 700K citizen scientists have joined the Folding@home project. This 20-fold increase in participation has given us unprecedented compute power to bring to bear on COVID-19. In fact, Folding@home is the first computer to achieve the exaFLOPS scale and is now estimated to be more powerful than the next top 100 supercomputers combined.

(...)

 

Read the whole story...

 

 

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"Where darkness shines like dazzling light"   —William Ashbless


Rene K wrote:

Demogorgon monster from the television series Stranger Things, so we’ve taken to calling the spike the COVID-19 Demogorgon.

 

 

 


haha this is the best part. A lot of this stuff brings back my virology and immunology lessons.

 

I don't read much about the rona anymore but my cleaning lady stole about a month's supply of TP from me last week and I can't decide if I'm going to fire her. I probably will but it's been nagging at me for the last few days that I'm firing someone over TP. So stupid. I would have given her some if she asked me. I'm firing someone over TP, friggin TP. My god I can't decide if this is peak Karen stuff.


Jennifer M wrote:

Rene K wrote:

Demogorgon monster from the television series Stranger Things, so we’ve taken to calling the spike the COVID-19 Demogorgon.

 

 

 


haha this is the best part. A lot of this stuff brings back my virology and immunology lessons.

 

I don't read much about the rona anymore but my cleaning lady stole about a month's supply of TP from me last week and I can't decide if I'm going to fire her. I probably will but it's been nagging at me for the last few days that I'm firing someone over TP. So stupid. I would have given her some if she asked me. I'm firing someone over TP, friggin TP. My god I can't decide if this is peak Karen stuff.


It's not the toilet paper you would be firing her for...it's the theft. I would fire someone who has stolen from me even if it were a dime. I could never trust them again in my home.

Catherine M wrote:


It's not the toilet paper you would be firing her for...it's the theft. I would fire someone who has stolen from me even if it were a dime. I could never trust them again in my home.


Yeah, it's not what she stole. It's that she  deliberately waited until I was in the shower and took it. This was after I had a convo with her about how happy I am that her family is ok and safe. I really liked her, but **Edited for Community Guidelines** I guess. The trust is gone so now I gotta find someone else. First world problems. 😢

researchediting
Community Member

Thanks, René! Setting up my spare rig now.

gilbert-phyllis
Community Member

I'm folding! Thanks, Rene!

 

 

-> You Can Help Now! 

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

https://twitter.com/foldingathome/status/1248329481594507265

 

Today’s #FAHPastSuccesses is a great example of how simulation data can be used to find drugs that bind to hidden (cryptic) pockets! pic.twitter.com/lRXrOVzlH6

— Folding@home (@foldingathome) April 9, 2020Capture d’écran 2020-04-10 à 15.23.12.jpg

Coronavirus – What we’re doing and how you can help 

 

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

Start now!

 

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"Where darkness shines like dazzling light"   —William Ashbless

Some update from the battlefront (April 13, 2020):

 

The Huang lab from the Hong Kong University of Science and Technology has released a series of Folding@Home projects to simulate the nsp12 and nsp14 complex.  We will screen existing FDA-approved NTP analog drugs. We aim to repurpose drugs that can inhibit SARS-CoV-2 replication.  

Read more...

 

Join the battle and do some science!

 

Figure_1-1.png

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

https://twitter.com/foldingathome/status/1250189646451085313

 

Hooray for more #FAHMeetTheProteins! Today, we’re featuring the SARS-CoV2 spike protein. This critical player in the virus’s lifecycle is already the target of many drug discovery and vaccine development studies.

 

EVmO1wTXkAIOox1.png

 

Help Now !

 

 

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

Here's my current score:  1,804,180

 

Capture d’écran 2020-04-15 à 17.10.56.jpg

Catch (on) me if you can!

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

Fold proteins, find a cure against COVID-19, win a prize!

 

Start folding...

...win a prize! 

 

 

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"Where darkness shines like dazzling light"   —William Ashbless

Great idea. I am now WU gathering.


Rene K wrote:

Here's my current score:  1,804,180

 

Capture d’écran 2020-04-15 à 17.10.56.jpg

Catch (on) me if you can!

 

 


I am so far behind! But now with a goal to shoot for. My firewall was interfering and I was offline a few days until I had time to get that sorted. Now up and running again.

 

avirockx007
Community Member

Great info for sure..!!! Good job.

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