OpenMM User Profile: Jesus Izaguirre, PhD

Notre Dame’s Jesus Izaguirre collaborates with Simbios to increase the time scales of protein folding simulations with OpenMM. Why team up with Simbios? Because “they are working on exciting problems and have good people,” he says.



Jesus Izaguirre, PhD, associate professor of computer science and engineering at the University of Notre Dame in Indiana, says the best thing about Simbios is the people. From mid-2006 to early 2008, Izaguirre spent a sabbatical at Stanford working largely with Vijay Pande. He has since returned to Stanford to attend several workshops, give Simbios seminars, and discuss further collaborations with Simbios PI Russ Altman and Simbios post-doc Sam Flores. “I want to work with them because they are working on exciting problems and have good people who are both competent and nice.” He also likes the fact that, at Simbios, science drives technological developments. “That is key,” he says.


In 2008-09 Simbios provided seed funding for a collaboration between Izaguirre and Pande. Their goal: to speed up protein folding simulations from the microsecond to the millisecond time scale, where the most interesting motions for biology happen—for example, protein folding and conformational changes. To do this, Izaguirre’s and Pande’s groups have developed a methodology called NML (Normal Mode Langevin). It is now being imported into OpenMM to reap the benefits of GPU acceleration that OpenMM provides.


Izaguirre is particularly interested in how mutations affect protein folding. For example, certain mutations in the WW domain—a protein domain implicated in Alzheimer’s and cancer—speed up folding 1000-fold. To figure out why, Izaguirre’s team is using OpenMM and NML, as well as Pande’s Folding@Home program—which allows researchers to get statistics about the probabilities of different folding outcomes by generating thousands of simulations. “For WW mutants, we may be talking about 30,000 folding simulations,” he says. “Only Folding@Home lets us do that. So it’s a good combination: using Folding@Home plus OpenMM plus

our methodology that gives the additional speedups.”


Izaguirre says Simbios is a terrific initiative. “And I think it’s unique because even though I’m working mostly on the molecular level, Simbios includes problems that are of biomedical relevance at a range of scales from molecular to tissue and organ level. And I think it’s a good thing to have that kind of cross-fertilization. So I do hope it’s around for a very, very long time!”

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