ACMD Seminar: Computational Molecular Biology and SARS-CoV-2

Tuesday, September 14, 2021

A video of this talk is available to NIST staff in the Math channel on NISTube, which is accessible from the NIST internal home page.

Computational Microscopy of SARS-CoV-2

Rommie Amaro

Department of Chemistry and Biochemistry
University of California, San Diego

I will discuss our lab’s efforts, together with collaborators, to use computational microscopy to understand the SARS-CoV-2 virus in atomic detail, with the goals to better understand molecular recognition of the virus and host cell receptors, antibody binding and design, and the search for novel therapeutics.  I will focus on our studies of the spike protein, its glycan shield, its interactions with the human ACE2 receptor, our ACM Gordon Bell Special Prize winning efforts to model the SARS-CoV-2 virion, and escape variants.

Overcoming the Multiscale Computer Simulation Challenge for Biomolecular Systems

Gregory A. Voth

Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA

Advances in theoretical and computational methodology will be presented that allow us to simulate complex biomolecular systems across multiple length and time scales. At the heart of these concepts are methods for deriving more simplified coarse-grained (CG) models from their underlying detailed molecular structures and atomic-scale interactions. An important new component of our work has also been the concept of the “ultra-coarse-grained” (UCG) model and its associated computational implementation. In the UCG approach, the CG models can have internal states, much like quantum mechanical states. These internal states help to self-consistently quantify a more complicated set of possible interactions within and between the CG models, while still maintaining a high degree of simplification in the simulation. The UCG approach greatly expands the possible range of systems amenable to accurate computer modeling, i.e., quite heterogeneous systems, including complex self-assembly and aggregation processes involving many proteins. Applications to experimentally important targets such as virus capsids (HIV) and virus particles (SARS-CoV-2 virions) will be presented.

Note: This talk will be recorded to provide access to NIST staff and associates who could not be present to the time of the seminar. The recording will be made available in the Math channel on NISTube, which is accessible only on the NIST internal network. This recording could be released to the public through a Freedom of Information Act (FOIA) request. Do not discuss or visually present any sensitive (CUI/PII/BII) material. Ensure that no inappropriate material or any minors are contained within the background of any recording. (To facilitate this, we request that cameras of attendees are muted except when asking questions.)

Host: Barry Schneider