Scientists Create Important New Tool for Developing COVID-19 Treatments, Vaccines

The team has created a web resource that provides scientists an easy way to see the progress of the structural biology community in this area. It also includes the team’s assessment of the quality of the individual models and enhanced versions of these structures, when possible.

When the threat of the coronavirus became apparent, scientists worldwide responded at an unprecedented pace to determine the atomic structure of the virus and its protein constituents. Researchers are using the resulting structural models in a variety of applications, ranging from structure-based drug design to planning a range of biomedical experiments. For that reason, it is essential that the atomic models are as accurate as possible. Given the urgency of the pandemic, most of these structures are deposited in the Protein Data Bank, a global repository of macromolecular structures, before publication and peer review.

The members of the team at the university, who are experts in structure validation and interpretation, noticed opportunities to improve several SARS-CoV-2 models using state-of-the-art refinement approaches and created the new web resource which is updated with new structures every week, in sync with the Protein Data Bank. In some cases, the team has worked with the researchers who generated the original structure to ensure that the site contains the most accurate models. This team has longstanding experience in correcting biomedically important structural models – for instance, in the field of antibiotic resistance.

“We have carefully analyzed the available models of SARS-CoV-2 proteins and present the results with the aim of helping the broad biomedical community. Structural models are ultimately the interpretation of the original researchers and sometimes are suboptimal. This is why a second set of eyes to validate important structures is so crucial,” said Wladek Minor, of UVA’s Department of Molecular Physiology and Biological Physics.

“In most cases, only minor corrections could be suggested. However, in several cases, the revisions were significant, especially in the sensitive area of protein-ligand complexes that are critical for follow-up research, like drug discovery work. The current health crisis demands that all SARS-CoV-2 structures are of the highest quality possible,” added Minor.

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University of Virginia School of Medicine