Dmitry Korkin — Professor of bioinformatics and computational biology at Worcester Polytechnic Institute (WPI). His group reconstructed the 3D structure of SARS-CoV-2's major viral proteins early in 2020 and made the structural genomics data openly available to researchers.
The gist
Lex Fridman talks with Dmitry Korkin during the early COVID-19 pandemic about the computational biology of coronaviruses. Korkin describes viruses as efficient, intelligent-seeming machines and walks through how a virus infects a cell via the spike protein and ACE2 receptor. He explains how his lab used the viral genome and the open Protein Data Bank to model SARS-CoV-2's proteins, identify mutated regions, and predict which existing drug compounds might still work. The conversation also covers protein folding, agent-based epidemic simulation (including a 'zombies on a cruise ship' project), masks, and Korkin's path from Russia into science.
Big reveals
- Korkin frames a virus not as a living organism but as a perfected, almost intelligent machine.
- Folding@home gamers produced better protein structures than scientists themselves, a profound result.
- Evolution doesn't mutate the viral genome uniformly; it targets very specific proteins while others stay nearly identical to SARS.
- A key finding: drug-binding sites on the new virus are largely unmutated, so existing small-molecule drugs may still work.
- Korkin singles out remdesivir as perhaps the most promising antiviral candidate.
- His five-year agent-based simulation project, codenamed 'zombies on a cruise ship,' became eerily relevant as the Diamond Princess outbreak unfolded.
- For the first time they modeled the pathogen itself as an explicit agent, not just the human hosts.
- Korkin notes he would have to renounce his US citizenship to easily travel back to Russia, making return difficult.
Things worth remembering
- SARS-CoV-2's R0 is estimated at 1.5-3, versus 5-7 for smallpox and 15+ for measles.
- The asymptomatic population matters because those people still shed and spread the virus.
- SARS-CoV-2 has at least 29 proteins, versus roughly 8-9 for influenza.
- The spike protein forms a trimer (three copies) to function as the virus's anchoring unit.
- A single virion is around 100 nanometers and may carry roughly 5,200 spike proteins.
- The first Protein Data Bank was reportedly organized on flash cards.
- The Contagion movie's virus was designed by virologist Ian Lipkin based on Nipah virus, detailed enough for Korkin's class to model.
- A recent study found tears are not contagious, with no viral shedding through tears.
- Masks work both ways: protecting the wearer and preventing an asymptomatic carrier from spreading the virus.
- Korkin collects scientist bobbleheads, starting with Watson and Crick and culminating with his favorite, Rosalind Franklin.
Recommended in this episode
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