‘Game-changing’ study offers a powerful computer-modeling approach to cell simulations

A milestone report from the University of Kansas appearing this week in the Proceedings of the National Academy of Sciences proposes a new technique for modeling molecular life with computers.

According to lead author Ilya Vakser, director of the Computational Biology Program and Center for Computational Biology and professor of molecular biosciences at KU, the investigation into computer modeling of life processes is a major step toward creating a working simulation of a living cell at atomic resolution. The advance promises new insights into the fundamental biology of a cell, as well as faster and more precise treatment of human disease.

“It is about tens or hundreds of thousands of times faster than the existing atomic resolution techniques,” Vakser said. “This provides unprecedented opportunities to characterize physiological mechanisms that now are far beyond the reach of computational modeling, to get insights into cellular mechanisms and to use this knowledge to improve our ability to treat diseases.”

Until now, a major hurdle to modeling cells via computer has been how to approach proteins and their interactions that lie at the heart of cellular processes. To date, established techniques for modeling protein interactions have depended on either “protein docking” or “molecular simulation.”

According to the investigators, both approaches have advantages and drawbacks. While protein docking algorithms are great for sampling spatial coordinates, they do not account for the “time coordinate,” or dynamics of protein interactions. By contrast, molecular simulations model dynamics well, but these simulations are too slow or low-resolution.

“Our proof-of-concept study bridges the two modeling methodologies, developing an approach that can reach unprecedented simulation timescales at all-atom resolution,” the authors wrote.

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