Modeling biomolecular kinetics with large-scale simulation
1Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Box 800886, Charlottesville, VA, 22908, USA; Department of Cell and Molecular Biology, Uppsala University, Box 256, Uppsala 75105, Sweden.
Abstract:
The molecular details of biomolecular kinetics present a challenging estimation problem because the identities of relevant intermediates and the rates of exchange between them must be determined. These can be derived from prior knowledge, but in recent years, great advances have been made in the development and application of methods to systematically determine states and rates using biomolecular simulation. Doing this for biological systems of reasonable complexity requires substantial computational power, and contemporary methods leverage distributed computing or leadership-class computing resources to accomplish this. The result has been substantial insight into pressing contemporary problems, including structural activation of pandemic viruses. Here, we highlight recent developments in both methodology and exciting applications.
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