CellPACK: A virtual mesoscope to model and visualize structural systems biology

Graham T. Johnson, Ludovic Autin, Mostafa Al-Alusi, David Goodsell, Michel F. Sanner, Arthur J. Olson

Research output: Contribution to journalArticle

43 Citations (Scopus)

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/.

Original languageEnglish (US)
Pages (from-to)85-91
Number of pages7
JournalNature Methods
Volume12
Issue number1
DOIs
StatePublished - Jan 1 2014

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Biological Models
Systems Biology
Structural Models
Human Immunodeficiency Virus Proteins
Mycoplasma
Synaptic Vesicles
Cell Biology
Molecular Biology
Cytoplasm
HIV
Cytology
Molecular biology
Biological systems
Graphical user interfaces
Blood
Plasmas
Proteins

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Johnson, G. T., Autin, L., Al-Alusi, M., Goodsell, D., Sanner, M. F., & Olson, A. J. (2014). CellPACK: A virtual mesoscope to model and visualize structural systems biology. Nature Methods, 12(1), 85-91. https://doi.org/10.1038/nmeth.3204
Johnson, Graham T. ; Autin, Ludovic ; Al-Alusi, Mostafa ; Goodsell, David ; Sanner, Michel F. ; Olson, Arthur J. / CellPACK : A virtual mesoscope to model and visualize structural systems biology. In: Nature Methods. 2014 ; Vol. 12, No. 1. pp. 85-91.
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Johnson, GT, Autin, L, Al-Alusi, M, Goodsell, D, Sanner, MF & Olson, AJ 2014, 'CellPACK: A virtual mesoscope to model and visualize structural systems biology', Nature Methods, vol. 12, no. 1, pp. 85-91. https://doi.org/10.1038/nmeth.3204

CellPACK : A virtual mesoscope to model and visualize structural systems biology. / Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David; Sanner, Michel F.; Olson, Arthur J.

In: Nature Methods, Vol. 12, No. 1, 01.01.2014, p. 85-91.

Research output: Contribution to journalArticle

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