In total, the researchers simulated 2.5 milliseconds a virtual eternity in chemical reaction time, the authors said of the receptor shifting from "on" to "off," capturing every viable configuration of atoms in between. These intermediate structures can then be experimentally confirmed, Pande said, but even before that happens, they can guide more efficient drug design. In particular, the authors have shown that different classes of drugs are preferred by different intermediate GPCR states.
"There is some tension right now between doing this type of work with specialized hardware or with general commodity hardware, as we have done," Pande said. "Cloud resources are much more accessible to the general scientific community, and I think that we've shown here that, with the right method and algorithms, you can do the same quality of work."
The next "ridiculous" challenge
The work grew out of a key project from Simbios, the NIH Center for Biomedical Computation at Stanford, a decade-old collaboration between a broad group of bioengineering, chemistry, biology and computer science faculty from Stanford and the Stanford School of Medicine.
"This work really represents a capstone to the molecular types of calculations that a diverse group of people can tackle, and it's a challenge that I thought was really pushing the limits," Pande said. "Ten years ago I would have said this is ridiculous; even five years ago it felt a little bit out of reach.
"But we brought together people who are really at the top of their game, and being around people like that really pushes you to be the best that you can."
Asked to project the next insane step in this research, something that might take another 10 years to unfold,
|Contact: Bjorn Carey|