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cellPACK Methods Paper

posted Dec 11, 2014, 5:29 PM by Graham Johnson   [ updated Dec 11, 2014, 5:42 PM ]
Image shows the cellPACK method of ultrastructure shells being packed with molecules, Jiri Klusak's HIV life cycle image, and a Mycoplasma Mycoides model
Our paper describing what cellPACK is and how it works was proudly published in Nature Methods January, 2015 issue.
Title: cellPACK: a virtual mesoscope to model and visualize structural systems biology
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/.
Authors: Graham T Johnson, Ludovic Autin, Mostafa Al-Alusi, David S Goodsell, Michel F Sanner, & Arthur J Olson
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