UW Bothell team using artificial intelligence to model atomic structure of coronavirus

A team led by a computer scientist at the University of Washington Bothell is using artificial intelligence to model the atomic structure of the COVID-19 coronavirus. The new software tool called DeepTracer could help design vaccines and drugs.

It uses deep learning to analyze a three-dimensional image of a virus protein molecule and trace the connections of its atoms.

"If you know the actual atomic structure of the viral protein you will know how to speed up the development of vaccines or drugs," said Dong Si, an assistant professor in the Division of Computing & Software Systems in the School of STEM.

DeepTracer uses images of the coronavirus that come from electron microscopes in cryogenic conditions in a process called 3D electron microscopy. To further refine the image, most researchers in the field use physics or traditional computational methods. "We are one of the first groups in the world to use deep learning to do this three-dimensional EM atomic protein complex structure prediction," Si said.

An independent outside expert in cryogenic electron microscopy who was asked to comment on DeepTracer, Carlos Oscar Sánchez Sorzano, a group leader of the Biocomputing Unit of the National Center for Biotechnology / Instruct Image Processing Center in Madrid, Spain, said it worked beautifully.

"You have filled the gap between cryo-EM maps at high resolution and atomic modelling from sequence in a very useful way that we hope opens new research lines leading to an even brighter future for the field," Sorzano said.

The DeepTracer website launched July 21, 2020. The project was supported with a $200,000 National Science Foundation Rapid Response Research grant (award 2030381).

More information:
www.uwb.edu/stem

research group: sites.google.com/uw.edu/dais-uw/home

public tool: deeptracer.uw.edu/home

award: www.nsf.gov/awardsearch/showAw … storicalAwards=false

Spain group: biocomputingunit.es

Maria Lamarca Anderson, mariala@uw.edu

Provided by University of Washington Bothell