Stanford University
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Derek Mendez
Staff Scientist - Biomedicine, Stanford Synchrotron Radiation Lightsource
Current Role at StanfordComputational staff scientist at the Stanford Synchrotron Radiation Lightsource (SSRL), in the Macromolecular Crystallography group (Structural and Molecular Biology division).
Main activities revolve around a 3 year BRaVE-funded project to build a new X-ray resource for the acceleration of medicines development (XMeD). Active in-silico areas of research are in the characterization of crystallization outcomes, virtual and experimental screening of ligands, in-silico methods for lead molecule optimization, and extremely sensitive absorption profile characterization using machine learning techniques. A major computational goal is to determine the most valuable tools (and develop new ones) for future XMeD users.
Beyond XMeD, we are focusing on using GPUs and machine learning models to accelerate processing and characterization of user diffraction data that is collected at SSRL beamlines 12-1, 12-2, 14-1, and 9-2. In addition, we are aiming to make available to users new methods that process X-ray diffraction data at the pixel-level in order to extract more information to better resolve structural changes in proteins arising from e.g., binding events and light/chemical driven dynamics.
We are also partnering with NERSC to build a framework for our beamline users to offload computationally intensive jobs to the Perlmutter GPU cluster.
