TCBG Seminar

“Garbage In, Garbage Out: Correcting -crystallographic errors through interactive molecular dynamics flexible fitting”

Dr. Tristan Croll
Queensland University of Technology
University in Brisbane, Queensland
Brisbane, Queensland

Thursday, February 26, 2015
3:00 pm (CT)
3269 Beckman Institute


Over the course of a complete re-refinement of the extracellular domain of the insulin receptor, I have adapted various tools available in VMD/NAMD (haptic-driven AutoIMD, MDFF, structural restraints, symmetry restraints etc.) into a single combined tool for the triage and, where necessary, complete re-refinement of crystal structures. The combination of high-quality visualization (and, equally importantly, the ability to easily hide extraneous information) coupled with the ability to physically interact in a realistic way with the problem region has proved extraordinarily powerful. Not only can even major structural errors be quickly resolved, but the crystallographic maps often contain substantial lower-resolution information to guide the placement of structures such as glycans and flexible loops that are typically left out by the crystallographer but are important to the modeler. With further development, I believe this method has the potential to both dramatically improve crystallographic results going into the future, and provide the modeling community with a user-friendly set of tools to put together the best possible starting models for their work.

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