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.affiliation: 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.
authors.forename: Graham T
authors.initials: GT
authors.lastname: Johnson
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Ludovic
authors.initials: L
authors.lastname: Autin
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Mostafa
authors.initials: M
authors.lastname: Al-Alusi
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: David S
authors.initials: DS
authors.lastname: Goodsell
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Michel F
authors.initials: MF
authors.lastname: Sanner
authors.affiliation: Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA.
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D006678:HIV / Q000648:ultrastructure; D006801:Humans; D008954:Models, Biological; D008967:Molecular Biology; D012984:Software; D049490:Systems Biology