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[email protected] latest projects are helping PC users fight COVID-19

These projects will help researchers to start 'rapidly developing new therapies' for Covid-19

Folding@home latest projects are helping PC users fight Covid-19

[email protected] latest projects are helping PC users fight COVID-19

The [email protected] project has just released a bunch of new CPU folding projects which will help PC users from across the world assist in vital research. Alongside existing COVID-19 simulations, the distributed computing project plans to help uncover which molecules will be able to effectively treat patients with the virus, enabling researchers to start "rapidly developing new therapies" against Coronavirus. 

This week, over 50 new CPU-based projects have been released to compliment [email protected]'s existing GPU-based COVID-19 projects. These new projects will estimate the affinity of potential drug molecules to attack COVIL-19's receptors. 
   
[email protected]'s Vincent Voelz describes these projects as "absolutely essential to our success", highlighting the potential of this research to uncover effective methods of treatment for Coronavirus patients. 

Below is [email protected]'s description of the project. 

 

    About the project

The Voelz and Chodera labs have been working with an international team of researchers to computationally screen potential inhibitors of the SARS-CoV-2 coronavirus main protease (also known as SARS-CoV-2 MPro or 3CL).  After the virus gets into a cell, it co-opts the cell’s translational machinery and makes a polyprotein (one long chain of amino acids) that needs to be cleaved into smaller pieces that become the functional parts of the virus.  The main protease is the viral protein that does the cleavage.

Timely high-throughput crystallization work by the Diamond Light Source XChem project has identified drug fragments that bind the protease, and now the race is on to use these initial hits to drive computational prioritization of compounds to synthesize.  We are using the power of [email protected] — now the largest supercomputer in the world — to screen tens of thousands of promising molecules that have been computationally docked to the protease.  These include over 6000 compounds designed and submitted as part of the COVID Moonshot challenge.  

About the calculations

We are using an alchemical free energy calculation method called free energy perturbation, or FEP, to estimate the affinity of a potential drug molecule to its receptor.  FEP methods are very expensive compared to other methods like docking, but with the advantages of high accuracy and physical insight.  We are using protocols very similar to those used in the most recent SAMPL blind challenge
The calculation involves decoupling the drug molecule (by turning off its electrostatic and dispersion interactions) from its receptor, and again for a molecule in water.  For the latter type of simulations, unfortunately there’s not much to look at the [email protected] viewer, because there’s no protein being simulated. However boring these projects appear, please keep in mind that they are absolutely essential to our success.

 

Folding@home latest projects are helping PC users fight Covid-19  

How can I help? 


Earlier this month, we released a guide on how to start Folding using Windows-based PCs. While Coronavirus-related projects are all GPU-based, CPUs are useful for existing projects for diseases like Alzheimer's, Huntington's, Parkinson's, and cancer. 

At this time, you cannot dedicate your PC's resources specifically to Coronavirus-related projects, but know that all of [email protected]'s projects are useful for disease research. 

For almost ten years, OC3D has hosted the Redline @ OC3D folding team (team number 98860). Those who are interested in folding should head over to our [email protected] subforum if you want to join the team or discuss folding with our active team members. 

You can join the discussion on [email protected] joining the fight against Coronavirus on the OC3D Forums

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Most Recent Comments

31-03-2020, 13:24:09

hmmblah
Thanks for the heads up, I turned on CPU slots for my Threadripper 1920X and Ryzen 3900X.Quote
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