Accelerating COVID-19 Research with GPUs

Key Takeaways

the stakes are high as scientists and researchers are racing the clock to find a cure the search for an antiviral depends on finding the right chemical structure that binds to the viral proteins like the RNA polymerase shown here and that prevents the virus from attaching or replicating to screen drug candidates researchers estimate the free energy of binding between the candidate molecule and the protein target using software like Auto doc the binding free energy is a measure of the effective strength of the interaction between the ligand and the protein and is a good lead indicator of activity calculating the free energy requires evaluating the pairwise interim ik potential between atoms of the potential drug and the protein target millions of times as the drug molecule is rotated translated bonds rotated and protein side chains moved exploring the huge conformational space in search of just the right fit producing the most favorable configuration for binding but the combinatorics is daunting even the largest chemical databases which contain billions of compounds only represent a tiny fraction of the number of possible small molecules any one of which may hold the cure this means scientists must screen billions of molecules searching for just the right activity here's a visual representation of screening a database of compounds when using a cpu evaluating millions of poses for billions of molecules would take even a supercomputer years on a single GPU this can be done more than 230 times faster than on a single CPU thread using all twenty seven thousand six hundred and forty eight GPUs of Summit researchers are able to screen more than 25,000 molecules per second allowing them to dock 1 billion compounds in less than 12 hours all told on each node of Summit auto-doc running six GPUs is more than 33 times faster than if it were running on all 44 CPU cores in the node the race to find a cure is on and GPUs are accelerating the scientific computing that's moving us closer to finding it