Episode
#90 – Dmitry Korkin: Computational Biology of Coronavirus
2:09:30
Published: Wed Apr 22 2020
Description
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. Support this podcast by signing up with these sponsors: - Cash App - use code "LexPodcast" and download: - Cash App (App Store): https://apple.co/2sPrUHe - Cash App (Google Play): https://bit.ly/2MlvP5w 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
Chapters
Professor Dimitris Agrafiotis discusses how computational methods can help us understand the biology of COVID-19 and other viruses in order to develop antiviral drugs and vaccines.
00:00 - 02:32 (02:32)
Summary
Professor Dimitris Agrafiotis discusses how computational methods can help us understand the biology of COVID-19 and other viruses in order to develop antiviral drugs and vaccines.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The speaker reflects on their understanding of the intelligence of humankind and artificial intelligence mechanisms, particularly in relation to the capacity of modern biotechnology to alter viruses.
02:33 - 10:21 (07:47)
Summary
The speaker reflects on their understanding of the intelligence of humankind and artificial intelligence mechanisms, particularly in relation to the capacity of modern biotechnology to alter viruses. They also contemplate the efficiency of viruses at the individual level versus society level.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Scientists studying influenza and coronavirus are constantly in an arms race to design vaccines that can combat evolving viruses, and creating a universal vaccine would be a significant advancement.
10:21 - 21:58 (11:36)
Summary
Scientists studying influenza and coronavirus are constantly in an arms race to design vaccines that can combat evolving viruses, and creating a universal vaccine would be a significant advancement. While the possibility of viruses jumping from one species to another is still an open question, designing a vaccine that can adapt to various strains would be a huge step forward.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Computational and data scientists are helping to generate a lot of information about cells through next-generation sequencing, transcriptomics, and live imaging that aids in understanding the complex protein interactions and drug mechanisms.
21:58 - 39:40 (17:42)
Summary
Computational and data scientists are helping to generate a lot of information about cells through next-generation sequencing, transcriptomics, and live imaging that aids in understanding the complex protein interactions and drug mechanisms.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Community efforts have contributed towards folding smaller proteins up to 100 residues, but folding larger proteins is still a challenge.
39:40 - 53:01 (13:20)
Summary
Community efforts have contributed towards folding smaller proteins up to 100 residues, but folding larger proteins is still a challenge. The folding at home project allows for individuals to contribute towards solving protein structures.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The study on the structures of proteins in a virus helps to understand how they interact with the host proteins and their evolution.
53:01 - 1:08:25 (15:24)
Summary
The study on the structures of proteins in a virus helps to understand how they interact with the host proteins and their evolution. The viruses attach to proteins in certain cells in the body, and scientists try to identify if they form protein complexes to perform a certain function.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The 3D structure of viral genomes can provide important information about the functional parts of a protein and how it has evolved.
1:08:25 - 1:17:13 (08:47)
Summary
The 3D structure of viral genomes can provide important information about the functional parts of a protein and how it has evolved. Mutations are not uniformly distributed across the entire viral genome, but rather target specific proteins.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Researchers are exploring the possibility of generating an overall virion model to better understand the structure of viruses and a potential live vaccine.
1:17:14 - 1:29:48 (12:33)
Summary
Researchers are exploring the possibility of generating an overall virion model to better understand the structure of viruses and a potential live vaccine. Ligand binding sites in the model show promise for an effective immune response without severe illness.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Scientist's discoveries of mini and maxi viruses have led to a reconsideration of how viruses originate and evolve, but it is still uncertain how this may affect the reopening of the economy during the pandemic.
1:29:48 - 1:37:09 (07:21)
Summary
Scientist's discoveries of mini and maxi viruses have led to a reconsideration of how viruses originate and evolve, but it is still uncertain how this may affect the reopening of the economy during the pandemic.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The origin of the virus can be traced back to a fruit bat and a pig.
1:37:09 - 1:47:18 (10:08)
Summary
The origin of the virus can be traced back to a fruit bat and a pig. Modeling infectious outbreaks can help us analyze and prevent such outbreaks, particularly on cruise ships which have suffered big losses due to cancellations caused by infectious outbreaks.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The first week is when a person, symptomatic or asymptomatic, is the most contagious, as the highest level of viral particles are shed during this time.
1:47:18 - 1:55:50 (08:32)
Summary
The first week is when a person, symptomatic or asymptomatic, is the most contagious, as the highest level of viral particles are shed during this time. There may also be a different rate of infection for asymptomatic individuals versus those who are symptomatic.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
The speaker talks about how he enjoyed biology, chemistry, physics, and math in high school, but his biggest passion was math, and how he realized that he wanted to apply his knowledge when he studied at Moscow State University.
1:55:50 - 2:01:41 (05:51)
Summary
The speaker talks about how he enjoyed biology, chemistry, physics, and math in high school, but his biggest passion was math, and how he realized that he wanted to apply his knowledge when he studied at Moscow State University.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Rosalind Franklin's famous photograph 51 played a crucial role in the discovery of the structure of DNA, and some argue that Maurice Wilkins would have solved it if he had access to it.
2:01:43 - 2:07:13 (05:29)
Summary
Rosalind Franklin's famous photograph 51 played a crucial role in the discovery of the structure of DNA, and some argue that Maurice Wilkins would have solved it if he had access to it. Additionally, Wilkins founded a school and was dedicated to educating the next generation of scientists.
Episode#90 – Dmitry Korkin: Computational Biology of Coronavirus
PodcastLex Fridman Podcast
Demetri Korkin emphasizes the fragility of human life and the need for society to bond together, thanks scientists for their work, and reminds us of the importance of viruses in the planet's genetic diversity.
2:07:13 - 2:09:10 (01:57)
Summary
Demetri Korkin emphasizes the fragility of human life and the need for society to bond together, thanks scientists for their work, and reminds us of the importance of viruses in the planet's genetic diversity.