[Folding@Home] Folding@Home Takes Up the Fight Against COVID-19 / 2019-NCOV - Overclock.net - An Overclocking Community
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[[email protected]] [email protected] Takes Up the Fight Against COVID-19 / 2019-NCOV

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post #1 of 88 (permalink) Old 03-10-2020, 10:46 AM - Thread Starter
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[[email protected]] [email protected] Takes Up the Fight Against COVID-19 / 2019-NCOV

Quote:
We need your help! [email protected] is joining researchers around the world working to better understand the 2019 Coronavirus (2019-nCoV) to accelerate the open science effort to develop new life-saving therapies. By downloading [email protected], you can donate your unused computational resources to the [email protected] Consortium, where researchers working to advance our understanding of the structures of potential drug targets for 2019-nCoV that could aid in the design of new therapies. The data you help us generate will be quickly and openly disseminated as part of an open science collaboration of multiple laboratories around the world, giving researchers new tools that may unlock new opportunities for developing lifesaving drugs.

2019-nCoV is a close cousin to SARS coronavirus (SARS-CoV), and acts in a similar way. For both coronaviruses, the first step of infection occurs in the lungs, when a protein on the surface of the virus binds to a receptor protein on a lung cell. This viral protein is called the spike protein, depicted in red in the image below, and the receptor is known as ACE2. A therapeutic antibody is a type of protein that can block the viral protein from binding to its receptor, therefore preventing the virus from infecting the lung cell. A therapeutic antibody has already been developed for SARS-CoV, but to develop therapeutic antibodies or small molecules for 2019-nCoV, scientists need to better understand the structure of the viral spike protein and how it binds to the human ACE2 receptor required for viral entry into human cells.
Source

As I am sure many of you are aware, the OCN Folding team holds it's monthly Foldathon's, and we are regularly giving away various prizes to participants. However, this month, with Stanford's announcement of this new research unit, Team 37726 is making a bigger push to have more and more individuals contribute to the cause. If you spare hardware cycles, from Noon EST March 16th - Noon EST March 18th, Team 37726 want's your help! Please stop by the March FAT thread for more information, and we are completely willing to assist you with getting the FAT client configured.

Every little bit counts!

https://www.overclock.net/forum/55-o...l#post28361158

EDIT [10MAR20 UPDATE]:

Quote:
This is an update on [email protected]’s efforts to assist researchers around the world taking up the global fight against COVID-19.

After initial quality control and limited testing phases, [email protected] team has released an initial wave of projects simulating potentially druggable protein targets from SARS-CoV-2 (the virus that causes COVID-19) and the related SARS-CoV virus (for which more structural data is available) into full production on Folding@home. Many thanks to the large number of [email protected] donors who have assisted us thus far by running in beta or advanced modes.

This initial wave of projects focuses on better understanding how these coronaviruses interact with the human ACE2 receptor required for viral entry into human host cells, and how researchers might be able to interfere with them through the design of new therapeutic antibodies or small molecules that might disrupt their interaction.

In the coming days, we hope to take advantage of some of the new structural biology and biochemical data that is being rapidly released by researchers around the world who are working to understand these viruses and strategies for defeating them. This work has been largely disseminated by preprint servers such as bioRxiv and chemRxiv, which aim to make research rapidly available to both other researchers and the public for other scientists to broadly evaluate and immediately start building on. We have also forged several new collaborations with other laboratories where we hope [email protected] will provide valuable support in COVID-19 research efforts.

While we will rapidly release the simulation datasets for others to use or analyze, we aim to look for alternative conformations and hidden pockets within the most promising drug targets, which can only be seen in simulation and not in static X-ray structures. We hope that these structures—once validated by emerging compound screening data—could help direct the virtual screening campaigns or the targeting of new pockets for which atomistic structures were not yet available.

Below, we provide short descriptions of the projects. Note that all input files are being made available on GitHub here for other researchers to take advantage of:

https://github.com/choderalab/coronavirus

This repository will evolve over the coming days as we add more projects and documentation. We will start posting datasets with structures on publicly available servers as soon as we have useful data to report.
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Last edited by Simmons572; 03-11-2020 at 07:54 AM.
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post #2 of 88 (permalink) Old 03-10-2020, 11:16 AM
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Nice! I heard they were going to be releasing the WUs soon to normal/advanced if they haven't already. You can count me in for the foldathon as usual!



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post #3 of 88 (permalink) Old 03-10-2020, 11:37 AM
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I haven't folded in a while, but this cause has inspired me. Is there a way to ensure that my cycles are contributed to COVID-19/2019-NCOV research?

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post #4 of 88 (permalink) Old 03-10-2020, 11:46 AM - Thread Starter
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Quote: Originally Posted by schmotty View Post
I haven't folded in a while, but this cause has inspired me. Is there a way to ensure that my cycles are contributed to COVID-19/2019-NCOV research?
As of right now, they haven't disclosed which new Work Units are being directed towards this cause. The rumors I've been seeing have been stating that the new Corex22 units may be related, but it has not been confirmed yet. From what I have been reading though, they are going to be upping the distribution of these new WU's in order to push priority research to the COVID-19 proteins.

EDIT:

Quote: Originally Posted by valvehead View Post
There is a thread in the beta forum listing the new projects for COVID-19:

Quote:
11741: Coronavirus SARS-CoV-2 (COVID-19 causing virus) receptor binding domain in complex with human receptor ACE2. atoms: 165550, credit: 15396

11742: Coronavirus SARS-CoV-2 (COVID-19 causing virus) protease in complex with an inhibitor. atoms: 62227, credit: 9405

11743: Coronavirus SARS-CoV-2 (COVID-19 causing virus) protease - potential drug target. atoms: 62180, credit: 9405

11744: Coronavirus SARS-CoV (SARS causing virus) receptor binding domain trapped by a SARS-CoV S230 antibody. atoms: 109578, credit: 7608

11745: Coronavirus SARS-CoV (SARS causing virus) receptor binding domain mutated to the SARS-CoV-2 (COVID-19 causing virus) trapped by a SARS-CoV S230 antibody. atoms: 110370, credit: 7685

11746: Coronavirus SARS-CoV-2 (COVID-19 causing virus) receptor binding domain in complex with human receptor ACE2 (alternative structure to 11741). atoms: 182699, credit: 16615
The post from yesterday stated that the projects would be moved to normal and advanced if there are no issues. They may already be available.

In another thread, people were asking about the possibility of selecting COVID-19 priority in FAHControl. Apparently this would require updating the program. Instead Stanford will likely set higher priority for the projects on their end, so we should just fold away.
This information was just posted in the March FAT thread. Thanks @valvehead

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post #5 of 88 (permalink) Old 03-10-2020, 11:57 AM
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I can confirm that no client-type flag is needed now. Two of my machines just received the new units.

There is a new update from Stanford here:


Quote:
This is an update on [email protected]’s efforts to assist researchers around the world taking up the global fight against COVID-19.

After initial quality control and limited testing phases, [email protected] team has released an initial wave of projects simulating potentially druggable protein targets from SARS-CoV-2 (the virus that causes COVID-19) and the related SARS-CoV virus (for which more structural data is available) into full production on Folding@home. Many thanks to the large number of [email protected] donors who have assisted us thus far by running in beta or advanced modes.

This initial wave of projects focuses on better understanding how these coronaviruses interact with the human ACE2 receptor required for viral entry into human host cells, and how researchers might be able to interfere with them through the design of new therapeutic antibodies or small molecules that might disrupt their interaction.

In the coming days, we hope to take advantage of some of the new structural biology and biochemical data that is being rapidly released by researchers around the world who are working to understand these viruses and strategies for defeating them. This work has been largely disseminated by preprint servers such as bioRxiv and chemRxiv, which aim to make research rapidly available to both other researchers and the public for other scientists to broadly evaluate and immediately start building on. We have also forged several new collaborations with other laboratories where we hope [email protected] will provide valuable support in COVID-19 research efforts.

While we will rapidly release the simulation datasets for others to use or analyze, we aim to look for alternative conformations and hidden pockets within the most promising drug targets, which can only be seen in simulation and not in static X-ray structures. We hope that these structures—once validated by emerging compound screening data—could help direct the virtual screening campaigns or the targeting of new pockets for which atomistic structures were not yet available.

Below, we provide short descriptions of the projects. Note that all input files are being made available on GitHub here for other researchers to take advantage of:

https://github.com/choderalab/coronavirus

This repository will evolve over the coming days as we add more projects and documentation. We will start posting datasets with structures on publicly available servers as soon as we have useful data to report.

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post #6 of 88 (permalink) Old 03-11-2020, 04:48 AM
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In, lets try to speed up tackling this one!

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post #7 of 88 (permalink) Old 03-11-2020, 07:56 AM - Thread Starter
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Quote: Originally Posted by valvehead View Post
There is a new update from Stanford here:
Great info, thanks mate

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post #8 of 88 (permalink) Old 03-11-2020, 09:39 AM
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I haven't folded in years but the setup seems much simpler now than it used to be. I was up and running on both cpu and gpu in less than a minute, I feel like I spent an entire evening getting it running before.

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post #9 of 88 (permalink) Old 03-11-2020, 11:45 AM
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Quote: Originally Posted by bigjdubb View Post
I haven't folded in years but the setup seems much simpler now than it used to be. I was up and running on both cpu and gpu in less than a minute, I feel like I spent an entire evening getting it running before.
Your 2080ti should get some great points too. I'm sure you are aware...but just checking.... make sure you use a passkey.




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post #10 of 88 (permalink) Old 03-11-2020, 11:59 AM
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I've only tried on the work computer so far (R5 3600 and Radeon VII) but I will get it running at home tonight. Are you referring to the "passkey" that they send you in your email?

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