#90 – Dmitry Korkin: Computational Biology of Coronavirus

Apr 22, 2020

Dmitry Korkin, a bioinformatics professor at Worcester Polytechnic Institute, sheds light on the computational biology behind COVID-19. He discusses his team's groundbreaking work in reconstructing the virus's 3D structure, crucial for vaccine development. The conversation also delves into the evolution of viruses, the challenges of creating a universal vaccine, and the importance of open data in scientific collaboration. Korkin explores the role of computational tools in understanding viral complexities, ultimately emphasizing the interplay between biology and technology.

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INSIGHT

Virus: An Intelligent Machine

Viruses, though not living organisms, resemble intelligent machines.
They possess a simple yet effective design, maximizing limited resources.

INSIGHT

Natural vs. Engineered Viruses

Natural viruses pose a greater threat than engineered ones due to their continuous evolution and emergence.
Dmitry Korkin expresses more concern for naturally occurring viruses.

INSIGHT

Smallpox Contagion

Smallpox has a higher R0 (5-7) than seasonal flu or COVID-19 (1.5-3), making it more contagious historically.
Measles is even more contagious with an R0 of 15 and above.

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Dmitry Korkin is a professor of bioinformatics and computational biology at Worcester Polytechnic Institute, where he specializes in bioinformatics of complex disease, computational genomics, systems biology, and biomedical data analytics. I came across Dmitry’s work when in February his group used the viral genome of the COVID-19 to reconstruct the 3D structure of its major viral proteins and their interactions with human proteins, in effect creating a structural genomics map of the coronavirus and making this data open and available to researchers everywhere. We talked about the biology of COVID-19, SARS, and viruses in general, and how computational methods can help us understand their structure and function in order to develop antiviral drugs and vaccines.

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EPISODE LINKS:
Dmitry’s Website: http://korkinlab.org/
Dmitry’s Twitter: https://twitter.com/dmkorkin
Dmitry’s Paper that we discuss: https://bit.ly/3eKghEM

This conversation is part of the Artificial Intelligence podcast. If you would like to get more information about this podcast go to https://lexfridman.com/ai or connect with @lexfridman on Twitter, LinkedIn, Facebook, Medium, or YouTube where you can watch the video versions of these conversations. If you enjoy the podcast, please rate it 5 stars on Apple Podcasts, follow on Spotify, or support it on Patreon.

Here’s the outline of the episode. On some podcast players you should be able to click the timestamp to jump to that time.

OUTLINE:
00:00 – Introduction
02:33 – Viruses are terrifying and fascinating
06:02 – How hard is it to engineer a virus?
10:48 – What makes a virus contagious?
29:52 – Figuring out the function of a protein
53:27 – Functional regions of viral proteins
1:19:09 – Biology of a coronavirus treatment
1:34:46 – Is a virus alive?
1:37:05 – Epidemiological modeling
1:55:27 – Russia
2:02:31 – Science bobbleheads
2:06:31 – Meaning of life