The lens is a software program he developed called DeepTracer, which can predict what the virus is made of, down to the smallest components — molecules and atoms.<\/p>\n\t\t\t\t
“Every day I wake up excited to work on this,” said Si. “I need to work on this every day to make it faster, better and more accurate.”<\/p>\n\t\t\t\t
Knowing the structure of the coronavirus — how the atoms line up, so to speak — is critical to drug developers.<\/p>\n\t\t\t\t
The information can create a more precise target for researchers seeking to disable or kill the virus.<\/p>\n\t\t\t\t
“If you know the actual atomic structure of the viral protein, you will know how to speed up the development of vaccines or drugs,” Si said.<\/p>\n\t\t\t\t
DeepTracer is available to anyone. Thousands have logged onto the website since it launched July 21.<\/p>\n\t\t\t\t
The UW Bothell team is one of a handful of groups around the world using artificial intelligence — machine learning — to explore and map the coronavirus.<\/p>\n\t\t\t\t
“Not too many people are working on this problem,” said Si, who began a project to map the coronavirus in February.<\/p>\n\t\t\t\t
Two weeks ago, the team — mostly UW students and one Seattle-area high school student — added a button to the website that lets the program display on a smartphone.<\/p>\n\t\t\t\t
Users can now gaze at the coronavirus when they’re sitting at the park or planted on the couch.<\/p>\n\t\t\t\t
![\"A](\"https:\/\/www.kentreporter.com\/wp-content\/uploads\/2020\/09\/22579822_web1_L2-200820-BothellVirusHBJ-FS.jpg\")
<\/a>A close look at a coronavirus model created by Dong Si and his students at UW Bothell. (Olivia Vanni \/ The Herald)<\/p><\/div>\n\t\t\t\t
According to independent <\/a>researchers<\/a>, DeepTracer’s accuracy for predicting the structure of the virus averages 84%. That’s a good day at the racetrack, but Si would like to bump that up to 99%.<\/p>\n\t\t\t\t DeepTracer is being used in particular to zero in on the protein spikes that jut from the surface of the virus.<\/p>\n\t\t\t\t A spike uses specific proteins to dupe human cell receptors into thinking it’s safe to open the door. (It’s like knowing the secret knock.)<\/p>\n\t\t\t\t If that occurs, the coronavirus hijacks the cell’s reproductive mechanism and the cell begins spewing copies of the virus.<\/p>\n\t\t\t\t Infection is the result.<\/p>\n\t\t\t\t Si has been working from his Woodinville home this summer, but on a recent morning he dropped into his small office at the UW Bothell campus to explain his work.<\/p>\n\t\t\t\t Computer programming books share the shelves with a half-dozen small, spongy balls — pink and purple models of an assortment of viruses and their spikes.<\/p>\n\t\t\t\t Si has been generating virtual models of viruses and their insides, including the Ebola virus, for 11 years. He admits: Biology wasn’t his strongest subject in high school. But while earning a Ph.D. in computer science, he discovered that computers could be harnessed to analyze bacteria and viruses.<\/p>\n\t\t\t\t DeepTracer uses 3D images of the coronavirus’s spike — taken by an electron microscope — to probe beneath the surface.<\/p>\n\t\t\t\t Enlarged millions of times, the spike resembles a knobby, gray cone.<\/p>\n\t\t\t\t While the image provides a glimpse of the spike’s surface and volume — if offers few clues to what lurks beneath.<\/p>\n\t\t\t\t Enter DeepTracer.<\/p>\n\t\t\t\t The program has been seeded with information about the structure of other viruses and macromolecules, which are large molecules composed of thousands of atoms.<\/p>\n\t\t\t\t Armed with a trove of existing models, maps and genetic sequences, DeepTracer’s artificial intelligence engine can predict which atoms are located where, Si said.<\/p>\n\t\t\t\t It’s akin to chess-playing software that uses information gleaned from millions of chess games to predict an opponent’s next move.<\/p>\n\t\t\t\t The resulting 3D model of the virus can resemble a structure made of Lego blocks. Specific atoms, such as oxygen and hydrogen, for example, are labeled with distinct colors so they can be easily identified.<\/p>\n\t\t\t\t Researchers and drug developers across the globe are “working day and night” to develop potent vaccines,” Si said.<\/p>\n\t\t\t\t The coronavirus isn’t the only bad bug DeepTracer is prepared to tackle, Si said.<\/p>\n\t\t\t\t “No matter what new bacteria or virus comes — tomorrow or next year — we will be able to model it quickly,” he said.<\/p>\n\t\t\t\t Janice Podsada; jpodsada@heraldnet.com; 425-339-3097; Twitter: JanicePods<\/em><\/p>\n\t\t\t","protected":false},"excerpt":{"rendered":" A team of computational scientists has developed web-based software that maps the virus’ protein spikes. <\/p>\n","protected":false},"author":603,"featured_media":47081,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[5,9,11,24],"tags":[89],"yst_prominent_words":[],"_links":{"self":[{"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/posts\/47080"}],"collection":[{"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/users\/603"}],"replies":[{"embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/comments?post=47080"}],"version-history":[{"count":0,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/posts\/47080\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/media\/47081"}],"wp:attachment":[{"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/media?parent=47080"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/categories?post=47080"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/tags?post=47080"},{"taxonomy":"yst_prominent_words","embeddable":true,"href":"https:\/\/www.kentreporter.com\/wp-json\/wp\/v2\/yst_prominent_words?post=47080"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}