Welcome to the Levitt Lab!
Since 28 January 2020, Levitt, his Stanford group and an international team of volunteers have worked tirelessly on data analysis of COVID-19. While widely distributed, our work has been hidden from search engines due to failure of our 25-year old lab website at www.csb.stanford. Follow us on Twitter. Relevant links follow:
14 Mar. Analysis of China and Rest of the World. This is a key analysis full of Tables and Figures that is not easy to comprehend; it is the basis of all my subsequent work.
22 Mar. LA Times Interview with Joe Mozingo
Why this Nobel laureate predicts a quicker coronavirus recovery: ‘We’re going to be fine’
22 Mar. The Medium, a first post on the Excess Burden of Death associated with coronavirus. This is for saturation of infection, like that on the Diamond Princess which may lead to herd immunity.
16 Apr. Particularly clear Radio New Zealand interview with Dave Campbell:
'No evidence that Covid-19 is causing huge loss of life' (listen)
2 May. Lockdown TV in London, James Billot & Freddie Sayer. Nobel prize-winning scientist: the Covid-19 epidemic was never exponential
15 May. Two YouTube podcasts
One of our team members Dr. Patrick Tam (retired Standard and Chartered Bank CIO living in Hong Kong) and his family have set up a remarkable website called Covibes.
Another early collaborator also from 7 Feb 2020 is Dr. Francesco Zonta at ShanghaiTech University. Francesco is heavily involved.
Now most of my group at Stanford are involved with COVID-19 as follows: Andrea Scaiewicz, Joao Rodrigues, and Frederic Poitevin.
Is it possible to understand the molecular structure and function of proteins and nucleic acids in enough detail to make accurate predictions about structure and function? We are mounting a two-pronged attack on this problem using both molecular dynamics simulation and molecular modeling. (i) Simulation attempts to reproduce the structural, thermodynamic and dynamic properties of a macromolecule in as accurate a way as possible. Starting with simple but realistic expressions for the interactions between atoms and classical laws of motion, we calculate a trajectory that specifies the position and velocity of every atom as a function of time. The time-step between calculated structures is small at 10-15 seconds, and we need to reduce hundreds of thousands of sets of atomic coordinates into a simple coherent description. We have simulated with reasonable fidelity the measurable static and dynamic properties of the several different proteins surrounded by thousands of water molecules. Simulation at different temperatures has allowed exploration of the pathways of protein denaturation of entire proteins and small fragments of protein secondary structure (alpha-helices and beta-hairpins). Companion studies of DNA double-helix segments in solution preserve the classical double helix while still showing a wide repertoire of interesting motions. (ii) Molecular modeling attempts to build a model of a macromolecule using known three-dimensional structures and energy minimization as complementary guidelines. Specific examples of this work include the automatic modeling of antibody variable domains, the general modeling of homologous proteins and studies of DNA base-pair mismatches. Questions we are trying to answer include: How can a protein be stabilized by a single amino acid change? How does the sequence of DNA cause local variations of double-helix conformation and stability? Extensive use is made of sophisticated programming, sequence and structural data bases, and computer graphics.