Breakthrough software can generate 3D models of a single cell

Researchers reveal new 3D modelling software that can construct accurate models of single cells and even viral particles at unprecedented detail.

by John Tyburski

Copyright © Daily Digest News, KPR Media, LLC. All rights reserved.

First published at Daily Digest News on December 2, 2014

The microbiology world is taking a look into viruses and bacteria at a level of detail not achieved before, thanks to a new 3D software package called cellPACK, developed by researchers at The Scripps Research Institute (TSRI). The development team demonstrated how well it works by modeling an individual HIV particle. The scientists anticipate that the software will advance microbiology research.

“We hope to ultimately increase scientists’ ability to target any disease,” said senior author Art Olson, professor and Anderson Research Chair at TSRI.

With the new software, researchers can examine viral and cellular structures on the medium “mesoscale” level, a size range between a collection of atoms to the micrometer scale. For reference, a human red blood cell is typically six to eight micrometers across its long axis. Mesoscale models of viruses, bacteria, and mammalian cells have up to now been painstakingly constructed manually.

To demonstrate cellPACk’s relevance, creators modeled the outer “spike” proteins of HIV and found that the modeled virus disagreed with predictions made by “gold standard” conventional, evidence-based methods. The cellPACK model shows that, in fact, spike proteins are distributed over the viral surface in a determined pattern rather than randomly as commonly thought.

“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.”

The new software is available for download at autoPACK.org. A description of cellPACK’s development and applications was published online on Monday in the journal Nature Methods.