Open-source repository for COVID-19 drug-delivery simulation data

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The Molecular Sciences Software Institute has launched an open-source website that will allow biomolecular scientists from around the world to share computer-aided drug-testing simulations targeting the protein at the center of COVID-19.

“The nature of this pandemic requires rapid and flexible response. This repository, and the data within, are designed to get the information out quickly. Researchers really wanted to get their data out in front of other scientists even though it had not necessarily been through the peer review process yet,” said T. Daniel Crawford, lead director of the institute and a University Distinguished Professor in the Department of Chemistry, part of the Virginia Tech College of Science.

Under the leadership of Teresa Head-Gordon, a MolSSI co-director and a professor of chemistry, bioengineering, and chemical and biomolecular engineering at the University of California, Berkeley, the MolSSI team started work on the COVID-19 website about a month ago, after scores of scientists began discussing ways to share simulation modeling data they had on the coronavirus.

The hub allows biomolecular researchers to compare computational models of the COVID-19 virus and to share what findings the scientists have made on drug delivery to the host protein of the SARS-CoV-2 virus.

“If we’re all trying to act fast, we’ll want to focus on a certain class of drugs that are repurposed, they’ve already been through clinical trials for other diseases or related viruses,” Head-Gordon said. “You have known molecules, and you want to see if there are places on the target protein that you can disrupt.”

The MolSSI effort is aligned with the publication of a letter in the Journal of Chemical Information and Modeling calling for a shared, open-source resource to help battle the novel coronavirus that has shuttered governments and economies worldwide. The letter currently has nearly 200 signatories, including that of all eight MolSSI co-directors and its software scientists, which proposed an effort to break down competitive barriers that could get scientists ahead of the next virus pandemic. The MolSSI effort has also garnered a $200,000 National Science Foundation (NSF) RAPID COVID-19 grant for its quick response.

“These scientists have committed to openly sharing all of the data that they already have and the data they are currently collecting or developing about the virus, its structure, its properties, potential drug targets, and other types of therapeutics,” Crawford said.

The MolSSI, according to Crawford, is a multi-university institute viewed as a neutral party by the science community, making it an ideal central hub for such an open-source repository. The MolSSI Board of Directors quickly tasked three of the organization’s software scientists to design and build the COVID-19 Molecular Structure and Therapeutics Hub.

The MolSSI software scientists behind the hub website are Andrew Abi-Mansour, Samuel Ellis, Levi Naden, and Ben Pritchard. “The hub is designed so researchers of all specialties can find data most beneficial to them based on their starting point,” said Naden, project leader on the hub. “Focusing heavily on the targeting modalities which can disrupt the SARS-CoV-2 viral life and infection cycles, anyone can jump into their domain of expertise and get the inputs and outputs, they need to help contribute.”

Efforts to get the hub operational included collaborations with BioExcel, the European Union-based Centre of Excellence for Computational Biomolecular Research, and even CERN, the European Organization for Nuclear Research, operator of the largest particle physics laboratory in the world and a go-to group for mastering massive quantities of data, said Head-Gordon. She called the MolSSI’s hub a “worldwide effort.” As of this writing, 60 scientists from the United States and Europe have contributed modeling or simulation data. The institute is making strides to reach scientists in China, Korea, and Japan so that they may share data and in turn use findings already contributed to the website, said Head-Gordon.

“I’m actually quite proud of our team because since we got such an early jump, it turned out our colleagues in Europe heard about it and said, ‘Can we join your effort?’,” Head-Gordon added.

Naden added that the hub helps defeat two enemies: time and repetition. He and his team have spent the better part of a month working from 12- to 16-hour days and weekends to get the functional site up and going. “Everyone who has agreed to help with the site, to provide data, to give their experience and time to help curate and review data, to coordinate and reach out, have all done so in good faith,” Naden said. “The community understands the need for such a place and that it’s going to be a bit rough in the name of speed. However, they also genuinely want to help solve this pandemic, and so any politics, personal motivations, and disagreements have been set aside so we can get this resource and out as quickly as possible to maximize the efforts of the bimolecular community.”

The MolSSI was founded in 2016 by Crawford and his co-director colleagues with initial funding from the NSF. Its mission: Form a national team of software scientists to design and build software tools that can help researchers of all stripes tackle complex software projects that will impact basic research ranging from human health to climate change. Member universities, in addition to Virginia Tech and UC-Berkeley, include Iowa State University, Rice University, Rutgers University, the University of Michigan, Stony Brook University, and University of Southern California.

The COVID-19 outbreak has likely set a new path for the MolSSI, bringing together scores of unrelated biomolecular simulation research groups into a tighter community, foregoing competition, a long-term goal of Crawford’s. “[COVID-19] is not going to be our last virus. We’ve seen a lot of these coronaviruses, and I presume we will see more in the future, but this and next time we’ll be more organized and prepared for it,” Head-Gordon added.

Information from Virginia Tech Media Relations

         
 

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