Coronavirus: from genetics to molecular geometry, here’s what NASA supercomputers study

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As announced a few months ago, after setting aside some activities due to the coronavirus emergency, NASA made part of its supercomputers available to researchers studying the evolution of the pandemic in order to seek candidates for treatment and vaccine.

In this, the US space agency is not alone: The plan to combine IT resources in the battle against Covid-19 also involves the National Science Foundation, IBM, Hewlett Packard Enterprise, Amazon, Microsoft, the Department of Energy labs and other academic institutions.

Of the 64 projects currently entrusted to this IT “consortium”, those entrusted to the supercomputers at the Ames Research Center of the NASA are 4, and they range from the identification of genetic risk factors to the development of 3D molecular geometry.


Regarding the study of genetic risk factors, researchers are carrying out the genetic sequencing of patients in the various stages of the disease, to understand if there is a genetic predisposition for the development of acute respiratory syndrome, a known complication of Covid-19 which leads to the need for forced ventilation.

These data will be fed to NASA super PCs, in the hope of being able to glimpse a common thread that allows identifying the patients most at risk before they get worse. Another research team, led by Rafael Gomez-Bombarelli of MIT, is trying to create a machine learning algorithm capable of detecting molecules that could potentially inhibit attacks on cells by the new coronavirus.

To “train” it, we will use data obtained from laboratory experiments relating to 300,000 molecules that have given more or less good results against SARS in 2003, caused by a coronavirus very similar to the current one. The MIT software which will run on NASA supercomputers will produce 3D models of the molecules to predict how and if they will bind to the new coronavirus.


Later, the algorithm will be able to consult a catalog of existing drugs to find those that contain biologically active molecules against the new coronavirus, since drugs already approved by government agencies for the regulation of food and pharmaceutical products are the fastest solution to treat patients.

The third project studies the functioning of the spike protein, which allows the virus to penetrate inside the cells and therefore to replicate itself. The computational power of the supercomputers will be used in this case to simulate at the atomic level the behavior of the complex molecules that make up this protein, in order to identify its individual movements and changes, in order to better understand its interactions.


Finally, the latest project entrusted to NASA concerns the identification of biomarkers related to Covid-19: researchers will harness enormous computing power to identify RNA sequences from patient’s nasal swabs, which include both the patient’s genetic material and the new coronavirus and bacteria normally found in the human body, to understand what factors lead to serious outcomes of the disease.

In this field, the role of microRNAs could be particularly interesting, which could be activated by the new coronavirus in order to escape the immune system and replicate itself.



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https://www.hdblog.it/tecnologia/articoli/n521827/coronavirus-genetica-supercomputer-nasa/

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