Clustering and learning reaction coordinates directly using atomic positions

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• Prof Glen Hocky, New York University
• Monday 21 November 2022, 14:00-14:30
• Zoom link: https://zoom.us/j/92447982065?pwd=RkhaYkM5VTZPZ3pYSHptUXlRSkppQT09.

If you have a question about this talk, please contact Jerelle Joseph.

To give meaning to biomolecular processes observed in simulation, we need to characterize the conformational ensemble in terms of transitions between metastable states. Extensive work has been done to discover the metastable states through clustering. Most recent approaches perform dimensionality reduction on a large set of internal coordinates, followed by a clustering technique. In recent work, we demonstrated that high quality clustering can be performed through Gaussian Mixture Models directly on positions through a maximum likelihood approach, if structural alignment is performed in an iterative fashion that takes into account covariances between residue positions. Following these developments, we demonstrate that dimensionality reduction performed on positions after this procedure is a promising technique for developing new reaction coordinates between states.

This talk is part of the Lennard-Jones Centre series.

This talk is included in these lists:

• Hanchen DaDaDash
• Lennard-Jones Centre
• Zoom link: https://zoom.us/j/92447982065?pwd=RkhaYkM5VTZPZ3pYSHptUXlRSkppQT09

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