New structural biology software tackles viruses and bacteria

cellPACK software can generate models of midsized structures, like this one of HIV.--Illustration courtesy of Scripps

The Scripps Research Institute in La Jolla, CA, has come up with some new 3-D modeling software that can more easily spotlight a set of midsized biological structures--like a virus or bacteria.

Dubbed cellPACK software, the researchers at Scripps went after a difficult target in structural biology, angling for the medium-sized scale of structures that fall somewhere between large (like cells) and small (like proteins.) And it moves work in the field from helping hands to the computer screen so investigators can do the work more quickly.

By modeling how viruses like HIV work, investigators can test various theories on how they work, and how they can can be quelled. And in a demo of the new technology Scripps says it modeled the distribution of "spike" proteins on the surface of the immature HIV. Their conclusion: A theory that the distribution of proteins was random could not be correct.

Their work was partially funded by the NIH.

Art Olson

"We hope to ultimately increase scientists' ability to target any disease," said Art Olson, a professor and Anderson Research Chair at Scripps, who is also the senior author of the new study. Olson and his colleagues are now tweaking the software for wider use.

"With the creation of cellPACK, Dr. Olson and his colleagues have addressed the challenge of integrating biological data from different sources and across multiple scales into virtual models that can simulate biologically relevant molecular interactions within a cell," said Veersamy Ravichandran of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research. "This user-friendly tool provides a new platform for data analysis and simulation in a collaborative manner between laboratories."

- here's the release