Folding plans to test for Covid-19

CORONAVIRUS PROJECTS coming to BETA

by rafwiewiora » Mon Mar 09, 2020 8:08 pm

Thank you all for your patience as we spent a week deciding on how to best use the awesome extra power we've gotten from all you folks wanting to help out with the coronavirus effort. We've settled on 6 projects for now, and there's a lot of new biochemistry data coming in that we'll most likely set up more projects with.

Here are short descriptions of the projects -- please give us a few more days to get you a full blog post explaining more biochemistry and what your work can achieve with these projects. In general, we're looking for alternative conformations and hidden pockets within the most promising drug targets, which can only be seen in simulation and not in static crystal / cryo-EM structures. There's some very fresh drug screening data coming out now for some of these, which we'll use to validate the simulations and help direct the screening efforts -- collecting as much data, as rapidly as possible will be crucial, and thank you again for making that possible!

All projects are using the new OpenMM GPU Core22.

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
 
Just signed up for the cause. Have also set my team ID to 10 now. There seems to be a definite lack of available work units available....has 8Pack been completing them all already?!
 
Cenedd said:
Just signed up for the cause. Have also set my team ID to 10 now. There seems to be a definite lack of available work units available....has 8Pack been completing them all already?!
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Just give it time. Servers have WU but are maxed out allocating then.

Sign up for Rosetta at home
 
Cheers ozaudio. Managed to get one of those this morning - it didn't play when I tried yesterday. Since joining the team my points show zero but I think that may just be down to the stats servers having a lie down as it just says "Bad Gateway" when I try....and that seems to be a known issue.

Freestream: The Rosetta home page seems to suggest they've done all they can regarding Corona....unless I'm utterly misreading it.
 
Cenedd said:
Cheers ozaudio. Managed to get one of those this morning - it didn't play when I tried yesterday. Since joining the team my points show zero but I think that may just be down to the stats servers having a lie down as it just says "Bad Gateway" when I try....and that seems to be a known issue.

Freestream: The Rosetta home page seems to suggest they've done all they can regarding Corona....unless I'm utterly misreading it.
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There are other stats websites out there. You won’t see stats until these websites update and you’ve submitted WU.

Secondly, if your referring to the Feb 24th post I wouldn’t assume that. Not delved too far into it to be honest.

I’ll have to look at the science when I get home more closely.
 
Hi Oz :)

I looked at the queue of jobs here: http://robetta.bakerlab.org/queue.php

Those that had COV in their Target description...
http://robetta.bakerlab.org/queue.php?id=&username=&target=COV

It shows these are all complete, but there could easily be lots of other C-19 work that just don't have COV in their Target description. Also, more work may get released at any time and typically these will have much shorter deadlines than the regular non C-19 work so will jump to the top of any queue you have and get processed quickly.

As with Folding@Home any work they are doing at Rosetta that isn't C-19 is still worthwhile research that helps our understanding in various diseases.
 
Taking the first entry in your list, the WU name starts rb_03_07_17144_17549...
rb just refers to the Robetta queue, 03 and 07 are month and date, 17144 is the Job ID which you can put into the first link in my previous post to search for the details, that takes you to this page: http://robetta.bakerlab.org/queue.php?id=17144&username=&target=

You can then click on the 17144 Job ID link to get details of what the work is about...
02OPao6.jpg

The next number in the WU name was the Domain ID (17549). If you hover your mouse over the Domain ID link it will show you whereabouts the work you are doing is located on the displayed model, you can also click on that link for another screen with more info.

If you actually want me to explain the science of each work unit that is above my pay grade :D
 
I should add that all those in your list have a deadline a week away, C-19 work is likely to have just a 1 or 2 day deadline so will disappear quickly as they will get worked on in preference to the ones with the longer deadlines.
 

Excellent, thanks.

PDW said:
I should add that all those in your list have a deadline a week away, C-19 work is likely to have just a 1 or 2 day deadline so will disappear quickly as they will get worked on in preference to the ones with the longer deadlines.
Click to expand...

Is there a way of ensuring that I get COVID-19 work next? I know all work is useful, however COVID-19 has my interest as my Mrs is out of work now unpaid for 8 weeks and potentially longer, so I have a vested interest in helping how I can.
 
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