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Nat Methods. 2015 Jan;12(1):85-91. doi: 10.1038/nmeth.3204. Epub 2014 Dec 1.

cellPACK: a virtual mesoscope to model and visualize structural systems biology.

Author information

1
1] Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA. [2] Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA. [3] California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California, USA.
2
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.

Abstract

cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.

PMID:
25437435
PMCID:
PMC4281296
DOI:
10.1038/nmeth.3204
[Indexed for MEDLINE]
Free PMC Article

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