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Unfolding Nature’s Secrets

Photo of David Baker

David Baker, UW Professor of Biochemistry

Professor David Baker’s groundbreaking work aims to unravel the mysteries of protein folding.

UW Professor David Baker and his team are using cutting-edge computing to unravel deep mysteries of how proteins function and unlock a world vastly different from our own.

It’s a world where treatments for viruses can be developed in weeks instead of years. Where cancer tumors can be eliminated quickly and completely. Where global warming can be tackled by neutralizing carbon dioxide, and antidotes can efficiently nullify toxins.

To make this world possible, Baker and his team seek to solve one of the greatest challenges in biochemistry today—understanding how proteins fold themselves into complex three-dimensional shapes that determine their function.

Naturally occurring proteins solved evolution’s challenges, said Baker, Director of the UW’s Institute for Protein Design, a world leader in this field. Unlocking their secrets will enable Baker and his team to design a new world of synthetic proteins to address 21st century challenges in medicine, energy and technology.

“Over billions of years, proteins solved all the problems that came up during evolution,” Baker said. “As we learn how to make new proteins with shapes we create, we can solve new problems we face today.”

Baker’s work is showing results. Examples include developing catalysts to potentially save vast amounts of energy in industrial processes, a drug being tested to neutralize gluten in food and a promising approach to vaccines for AIDS and Ebola.

This kind of research requires massive computing power, and that’s where UW-IT comes in. Baker’s team runs thousands of calculations daily that would have been impossible even five years ago. Today, UW-IT provides Baker with more than enough computing power to tackle the research.

Baker uses Hyak, UW’s shared high-performance research computing cluster, and lolo, the large-scale data archiving and collaboration service for researchers. He will be a major user of UW’s new 100G (Gigabits per second) High Speed Research Network, giving him ample computing capacity to handle vast amounts of data.

“Baker’s lab transfers about two petabytes from the Internet each year,” said UW-IT Research Computing Director Chance Reschke. “If this were digital music, it would take 4,000 years to play it.”

“Big-Data researchers like Baker have driven big improvements in UW computing infrastructure, with benefits for the entire academic community,” said Brad Greer, UW-IT’s Assistant Vice President for Computing Infrastructure. “Initially, we focused on building a capable, scalable infrastructure for large researchers like David,” Greer said. “Thanks to them, any UW researcher today, large or small, has access to incredible capabilities at very low cost.”

Perhaps the most surprising thing about Baker’s large-scale use of UW-IT computing resources is that he rarely gives it a thought. “It just works. It’s invisible. And as a researcher, that’s the way you want it,” Baker said. “The ease and speed keeps going up, and the cost keeps going down. And that really helps move our work forward.”