Folding@home latest projects are helping PC users fight COVID-19
Folding@homeÂ latest projects are helping PC users fight COVID-19
This week, over 50 new CPU-based projects have been released to compliment Folding@home’s existing GPU-based COVID-19 projects. These new projects will estimate the affinity of potential drug molecules to attack COVIL-19’s receptors.Â
Folding@home’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.Â
Below is Folding@home’s description of the project.Â
Â Â About the project
TheÂ VoelzÂ andÂ ChoderaÂ labs have been working with an international team of researchers to computationally screen potential inhibitors of theÂ SARS-CoV-2 coronavirusÂ mainÂ proteaseÂ (also known as SARS-CoV-2 MPro or 3CL).Â After the virus gets into a cell, it co-opts the cellâs translational machinery and makes aÂ polyproteinÂ (one long chain of amino acids) that needs to be cleaved into smaller pieces that become the functional parts of the virus.Â TheÂ main proteaseÂ is the viral protein that does the cleavage.
Timely high-throughput crystallization work by theÂ Diamond Light Source XChemÂ projectÂ 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.Â We are using the power of Folding@home â nowÂ the largest supercomputer in the worldÂ â to screen tens of thousands of promising molecules that have been computationally docked to the protease.Â These include over 6000 compounds designed and submitted as part of theÂ COVID Moonshot challenge.Â Â
About the calculations
We are using anÂ alchemical free energy calculationÂ method calledÂ free energy perturbation, or FEP, to estimate the affinity of a potential drug molecule to its receptor.Â FEP methods are very expensive compared to other methods like docking, but with the advantages of high accuracy and physical insight.Â We are using protocols very similar to those used in the most recentÂ SAMPL blind challenge.Â
The calculation involvesÂ decouplingÂ the drug molecule (by turning off its electrostatic and dispersion interactions) from its receptor, and again for a molecule in water.Â For the latter type of simulations, unfortunately thereâs not much to look at the Folding@home viewer, because thereâs no protein being simulated. However boring these projects appear, please keep in mind that they are absolutely essential to our success.
How can I help?Â
Earlier this month, we released a guide onÂ how to start Folding using Windows-based PCs. While Coronavirus-related projects are all GPU-based, CPUs are useful for existing projects for diseases likeÂ Alzheimer’s, Huntington’s, Parkinson’s, and cancer.Â
At this time, you cannot dedicate your PC’s resources specifically to Coronavirus-related projects, but know that all ofÂ Folding@home’s projects are useful for disease research.Â
For almost ten years, OC3D has hosted theÂ Redline @ OC3D folding teamÂ (team number 98860). Those who are interested in folding should head over to ourÂ Folding@homeÂ subforumÂ if you want to join the team or discuss folding with our active team members.Â
You can join the discussion onÂ Folding@homeÂ joining the fight against CoronavirusÂ on theÂ OC3D Forums.Â