Researchers hoping to discover what goes on inside bacteria, viruses, and other components inside the human body will be able to do so in greater detail than was ever possible before thanks to new software, its developers say.
One use of the software, dubbed cellPACK, could be to create models of viruses such as HIV by solving a major research problem common in structural biology, they say.
Scientists have techniques for studying either relatively large structures such as cells or very small structures like proteins, but have problems trying to visualize or model structures in a "mesoscale" or medium resolution.
The cellPACK software will allow scientist to quickly process data they've gathered on smaller structures to create research models in that mid-size range, a process that when done by hand can take weeks or even months.
With cellPACK, the same process can be completed in hours, says Art Olson of The Scripps Research Institute, senior author of a study reporting the software development in the journal Nature Methods.
"We hope to ultimately increase scientists' ability to target any disease," Olson says.
Development of cellPACK started as a thesis project of Graham Johnson when he was at Scripps. He is now on the faculty of the University of California, San Francisco.
With many years' experience working as a medical illustrator, Johnson hoped to create a quick and efficient way to visualize structures at the mesoscale level.
The cellPACK software is based on an earlier effort by Johnson known as autorPACK, a program for mapping the densities of materials such as red blood cells in an artery.
"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," says Veersamy Ravichandran of the National Institutes of Health's National Institute of General Medical Sciences, which partially funded the research.
Many other researchers have contributed to the ongoing development of cellPACK, offering the software as free and open source, available for download at https://www.autopack.org.
Ongoing input from the scientific community will help expand the software allowing it to model ever-increasing numbers of biological shapes, Olson says.
"Making it open source makes it more powerful," said Olson. "The software right now is usable and very useful, but it's really a tool for the future."
