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.
What this episode covers
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.
Recommended on this episode
The Ascent of Money
Niall Ferguson
“I recommend a cent of money as a great book on this history debits and credits on Ledger's started around 30,000 years ago”— Lex Fridman
Remdesivir
Gilead Sciences
“I think remedy severe is perhaps the most promising it has been shown to be an efficient and effective antiviral for SARS”— guest
Also referenced (named, not recommended)
Bitcoin
Satoshi Nakamoto
“Bitcoin the first decentralized cryptocurrency released just over ten years ago so given that history cryptocurrency is still very much in his early days”— Lex Fridman
Folding@home
Stanford University
“folding at home it was originally and I remember I was a postdoc and we learned about this game because it was originally designed as the game”— guest
Foldit
University of Washington
“kids are actually getting very good at folding the proteins and it was you know it came to me as the sort of manifest of our capacity”— guest
AlphaFold
DeepMind
“in the recent competition half a fault was among the top performing teams if not the top performing team so there is definitely a benefit”— guest
Contagion
Steven Soderbergh
“we actually modeled the virus from the contagion movie yes so MeV won and you know unfortunately that virus”— guest
Big reveals from this episode
- 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.
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.