Communications of the ACM
'blue Waters' Supercomputer Helps Crack Hiv Code
Researchers developed molecular simulations of the HIV capsid using data from lab experiments performed at the University of Pittsburgh and Vanderbilt University.
Credit: Elizabeth Fisler
University of Illinois at Urbana-Champaign researchers used the Blue Waters supercomputer to discover the structure of the HIV capsid.
The researchers developed molecular simulations that used data from lab experiments performed at the University of Pittsburgh and Vanderbilt University.
"The work of matching the overall capsid, made of 64 million atoms, to the diverse experimental data can only be done through computer simulation using a methodology we have developed called molecular dynamic flexible fitting," notes Illinois professor Klaus Schulten. "You basically simulate the physical characteristics and behavior of large biological molecules, but you also incorporate the data into the simulation so that the model actually drives itself toward agreement with the data."
The researchers found that the HIV capsid consists of 216 protein hexagons and 12 protein pentagons arranged just as the experimental data suggested. The proteins that comprise these pentagons and hexagons are identical, but from one region of the capsid to another, the angles vary.
"The sustained petascale performance of Blue Waters is precisely what enabled these talented researchers to explore new methods combined with structural and electron microscopy data to reliably model the chemical structure of the HIV capsid in great detail," says the U.S. National Science Foundation's Irene Qualters.
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