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August Update: OpenPandemics - COVID-19
13 Aug 2020   

Summary
OpenPandemics - COVID-19 launched in May, and the work has just begun. Learn more about the scientists' progress so far, as well as the collaborations that will help move the research forward in the coming weeks and months.

The OpenPandemics research team
Top: Stefano Forli, Paolo Governa, Andreas Tillack, Jérôme
 Eberhardt
Middle: Giulia Bianco, Batuujin Burendei, Diogo Santos-Martins, Martina Maritan
Bottom: Matthew Holcomb, Christina Garza

Click here to learn more about the team.

 

Background

OpenPandemics - COVID-19 was created to help accelerate the search for COVID-19 treatments. You can learn more about the details of the work on the research team's website.

Data analysis

Since OpenPandemics - COVID-19 launched in May, the project has screened millions of chemical compounds that may be potential treatments for the disease. The screening is still ongoing, but the research team has analyzed the results they've gotten so far (45.7 million runs and 2.3 billion poses), and have narrowed the initial group down to approximately 1,500 compounds (0.00003 % of the total ligands docked!) that have been selected for their interactions with the target proteins and that warrant further analysis.

From the current group of 1,500 compounds, the researchers will do manual analysis to identify approximately 100 of the most promising, which will then go to their collaborators for further laboratory testing. (You can see a list of collaborators toward the bottom of the Research Participants page.)

While this testing goes on, they'll continue analyzing the data they receive from us and will continue to send new work to us.

Additional collaborations

The principal investigator is in touch with the team of European scientists of the Coronavirus Structural Taskforce to help improve the quality of results for all basic research on SARS-CoV-2. The team is collecting and curating protein structural data available on the SARS-CoV and SARS-CoV2 viruses that is getting constantly produced by researchers all over the world. They refine the published data, and perform statistical validation and diagnostics on the structures to correct for experimental errors or fluctuations.

Grant award

The Forli lab recently received a Baxter Foundation Young Investigator Award for the identification of new chemical compounds as promising drug development candidates. 

GPU version

The World Community Grid development team is starting to create work units for initial alpha testing. Their current issue is creating work units that can run on both CPU and GPU, rather than needing to create two different versions, which would add complexity to the project. The next step within IBM will be a security review of the new version. The work is ongoing and there's currently no estimate for when it will be completed.

Potential publications

The researchers are working on several papers. One is a paper about the history of AutoDock (the software that runs OpenPandemics, which was created at Scripps Research). If the paper is accepted, it will be published early in 2021. 

They also submitted a paper describing the development and application of protocols for the study of covalent inhibitors (including the reactive docking protocol used in the OpenPandemics). 

Another paper has been submitted describing their collaborative work with the Oak Ridge National Laboratory team and NVIDIA to run simulations to identify new molecules against the SARS-CoV2 virus. 

Current status of work units

  • Available for download:  4,882 batches
  • In progress:  2,052 batches (16,101,394 work units)
  • Completed:  5,459 batches (2,587 batches in the last 30 days,
    an average of 86 batches per day)
  • Estimated backlog: 56 days

 

Click here to learn more about World Community Grid's monthly project updates.




Research Call Notes