In mid-November 2020, HPC5 enabled the most complex molecular supercomputing experiment to date to be carried out to identify new treatments for the virus. Everything took place as planned and on schedule, making it the largest study globally on the interaction of the virus with possible drugs. The data is currently being processed and the results will be made freely available to the scientific community.
The experiment, called the Fast Track phase, began on the evening of Friday, 19 November and ended on the morning of Monday, 21 November, for a total of 60 processing hours. The goal was to test the interaction of 71.6 billion molecules on 15 "active sites" of the virus. Therefore, a total of 1074 billion interactions equal to 5 million simulations per second were processed. The experiment generated 65 TeraBytes of results, i.e. 4.33 TB for each SARS-CoV2 site analysed.
To achieve this, 1,500 HPC5 nodes worked continuously. In total, the supercomputer deployed 6,000 high-performance GPU graphics cards, that are particularly well suited to the large mass of highly parallel calculations required for these simulations. The movement of the virus and its interactions with each molecule were reproduced on the computer to identify those molecules that interact best with the virus and manage to bind to it, neutralising it and preventing it from replicating itself by destroying the host cells.
The experiment simulated "molecular docking", i.e. all possible intermolecular links between virus proteins and other already known molecules among potentially usable drugs, natural products, nutraceuticals and other substances on the market from public databases and those made available by pharmaceutical companies. By processing the results of the screening, it is possible to identify candidate molecules, i.e. those capable of attacking the virus and locking it in and preventing it from unleashing its viral load. The aim is to have more effective drugs that have already been clinically tested and are therefore immediately available. HPC5 and the Marconi supercomputer by Cineca have a total computing capacity of 81.1 Petaflop/s , equivalent to 81 million billion floating point operations per second when taking both supercomputers into account.
In the first phase of the trial, from the start of the project until June 2020, HPC5 and three other supercomputers involved in the research conducted docking tests on over 400,000 molecules, including artificial drugs and natural products, made available by Dompé. This phase of the project ended with the identification of a molecule, Raloxifene, a drug used for the treatment of osteoporosis, which has demonstrated a potential effectiveness in blocking the replication of the virus within the cells.