OpenMM User Profile: Kim Branson, PhD

Kim Branson of Vertex Pharmaceuticals uses OpenMM as the GPU accelerator for Yank, a program for quickly estimating molecular binding affinities that he’s building with collaborators from Pande’s lab.

from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips

 

Kim Branson, PhD, a research scientist in the modeling and simulation group at Vertex Pharmaceuticals, together with John Chodera, PhD, a former Pande group member now at the University of California, Berkeley, are developing a program called Yank along with several other alumni of Pande’s lab.  “It’s become a focal point for everyone to contribute,” Branson says.

 

Yank, which is built on OpenMM, estimates the energy involved when a chemical entity binds to a protein target, a critical calculation in drug design. “OpenMM is absolutely critical for Yank,” he says, because it speeds up the calculations.  Industrial chemists don’t want to wait two weeks for a computational answer that will help design the next experiment, Branson says. “So we need to run these calculations in a day, which OpenMM allows us to do.”

 

Branson wants to make Yank user-friendly, so that chemists, including those at Vertex, can use it. And, like OpenMM, it will be open source and available on Simtk.org, which Branson uses as a centralized repository for all sorts of tools. “It’s actually in everyone’s best interest to have an open set of tools,” he says. The more people use a tool, the more it evolves as people contribute, provide feedback, and gain experience with what works and doesn’t work, he says. “Everyone wins.”
 



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