Multi-scale Dynamics: Molecules to Cells
Associate Professor Rommie Amaro, Principal Investigator, Amaro Lab, University of California (San Diego).
With exascale computing power on the horizon, computational studies have the opportunity to make unprecedented contributions to drug discovery efforts.
Steady increases in computational power, coupled with improvements in the underlying algorithms and available structural experimental data, are enabling new paradigms for discovery, wherein computationally predicted ensembles from large-scale biophysical simulations are being used in rational drug design efforts. Such investigations are driving discovery efforts in collaboration with leading experimentalists.
I will describe our work in this area that has provided key insights into the systematic incorporation of structural information resulting from state-of-the-art biophysical simulations into protocols for inhibitor and drug discovery, with emphasis on the discovery of novel druggable pockets that may not be apparent in crystal structures.
I will also discuss how we are developing capabilities for multi-scale dynamic simulations that cross temporal scales from the picoseconds of macromolecular dynamics to the physiologically important time scales of cells (milliseconds to seconds).
Our efforts are driven by gaps in current abilities to connect across scales where it is already clear that new approaches and insights will translate into novel biomedical research discoveries and therapeutic strategies.
Dr Rommie Amaro is the Principal Investigator of the Amaro Lab at the University of California (San Diego) and also the Director of the university’s National Biomedical Computation Resource.
In 2012, Dr Amaro opened her lab in UCSD’s Department of Chemistry and Biochemistry. Research in the Amaro Lab is broadly concerned with the development and application of state-of-the-art computational methods to address outstanding questions in drug discovery and molecular-level biophysics.
Her lab focuses mainly on targeting neglected diseases, Chlamydia, influenza, and cancer, and works closely with experimental collaborators to catalyse the discovery of new potential therapeutic agents.
The Amaro Lab is also keenly interested in developing new multi-scale simulation methods and novel modeling paradigms that scale from the level of atoms to whole cells, and beyond.