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3-D Bio Modeling, Illustration Software Designed

Proteins on HIV surface

Proteins illustrated on the surface of an HIV virus (

2 December 2014. Researchers at Scripps Research Institute in La Jolla, California developed cellPack, software that makes it possible to model and visualize biological matter in three dimensions between the levels of molecules and cells. The open-source software from the lab of Scripps computational biologist Arthur Olson is described in a paper published online yesterday in the journal Nature Methods (paid subscription required).

Olson and colleagues designed cellPack to fill a gap in structural and systems biology, where current technologies can study interactions at the level of molecules such as proteins and at higher levels such as cells, but not activities between those two levels. This intermediate or mesoscale level, say the authors, can model and represent biological structures and activity in a range of 10 to 100 nanometers; 1 nanometer equals 1 billionth of a meter.

The software allows for automated assembly of biological structures beginning at the molecular level, where researchers can generate alternative models by varying and testing their molecular make-up. The authors say the software handles data imported from multiple systems and structural biology sources, and can build complex 3-D models.

The cellPack project was started by the paper’s first author Graham Johnson, now on the faculty of  University of California in San Francisco. Johnson, who worked as a scientific illustrator for 15 years, adapted autoPack, an open-source software for testing algorithms that pack various ingredients into defined spaces, such as construction materials and even blood cells in a vein or artery. Like autoPack, cellPack assembles and analyzes structures from rules in models and algorithms that in this case simulate molecular interactions in a cell.

In the Nature Methods paper, the Scripps team modeled an HIV envelope protein, testing a hypothesis that the protein spikes on the surface of an immature HIV virus were random occurrences. With cellPack, the authors generated and tested a large number of models and presented data demonstrating the protein spikes were distributed according to a pattern that was not random.

Both cellPack and autoPack are offered as open-source software. The Web site offers packaged models for HIV, blood plasma, cytoplasm fluid within a cell, and vesicles in synapses — the long roots of nerve cells that emit neurotransmitter signals. The published paper also says the Scripps team devised models for mycoplasma cells, a type of bacteria without cell walls, which do not often respond to conventional antibiotics.

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