News article: Science at cusp of 'transformational' grasp of life via cell modeling, researchers say

posted Oct 25, 2016, 10:24 AM by Graham Johnson

A review published by Arthur Olson in the Journal of Molecular Biology highlights advances towards 3D models of whole cells.

The image from co-author Arthur Olson's lab at the Scripps Research Institute shows a preliminary model of mycoplasma mycoides. Modeling by Ludovic Autin and David Goodsell, rendering by Adam Gardner. Credit: The Scripps Research InstituteRead more at:

UC San Diego and TSRI Launch New Consortium to Create ‘Virtual Cell’

posted Oct 21, 2015, 5:36 PM by Graham Johnson

Drawing on complementary strengths, the University of California, San Diego and The Scripps Research Institute have formed a new consortium with a big mission: to map cells in space and time. The consortium will offer fellowship funding for 10 to 12 graduate students and postdoctoral fellows to work on collaborative projects that build bridges between the campuses and different disciplines to assemble and simulate a virtual model of a cell, down to an atomic level of detail. 

PSI & Nature's Structural Biology Knowledgebase features cellPACK

posted Mar 17, 2015, 8:49 PM by Graham Johnson

The Structural Biology Knowledgebase (SBKB), a collaboration between the Protein Structure Initiative and Nature Publishing Group, wrote an article entitled Molecular Portraits of the Cell to describe how "The cellPACK software generates there-dimensional mesoscale models for a detailed look at biological systems like the cell.  A followup to our Nature Methods article in their Research Advances, February 2015 Technical Highlights issue. SBKB [doi:10.1038/sbkb.2014.245]

Happy Holidays

posted Dec 17, 2014, 3:02 PM by Graham Johnson   [ updated Dec 17, 2014, 3:09 PM ]

M. mycoides in snow. Happy Holidays card image by Thao Do and Graham Johnson
Have a joyous winter break and enjoy this card that Mesoscope student intern Thao P. Do created in collaboration with Graham Johnson for the UCSF Chimera 2014 Holiday card as described by Tom Goddard and Elaine Meng from RBVI below. Click the USE tab to see how Chimera can be used to view and analyze cellPACK models. Please feel free to print the card for your emergency Holiday needs.

A cellPACK model of bacterium Mycoplasma mycoides 
Behold a computer-generated model of the tiny bacterium Mycoplasma mycoides. The long orange strand is its circular DNA genome, a million basepairs encoding about 1000 genes. This bacterium lacks a cell wall but is covered with lipoglycans, shown here as green filaments. In red, yellow, blue, and purple are various proteins, represented by the structures of homologous proteins from other organisms. Together, these depict the molecular crowding in cells. This model was made with the cellPACK* software ( described in cellPACK: A virtual mesoscope to model and visualize structural systems biology, Johnson et al., Nat Methods (2014). cellPACK models can be viewed interactively with the program UCSF Chimera ( from the Resource for Biocomputing, Visualization, and Informatics**

Funding: * NSF Predoctoral Fellowship (07576), NIH P41GM103426 & P50GM103368, Autodesk, & Mary Anne Koda-Kimble Seed Award for Innovation. ** NIH/NIGMS Biomedical Technology Research Center (P41GM103311). 

M. mycoides in Snow by RBVI associates Graham T. Johnson & Thao P. Do of and, ©2014

Science magazine Editors' Choice

posted Dec 11, 2014, 5:47 PM by Graham Johnson   [ updated Dec 11, 2014, 5:49 PM ]

CoverOur cellPACK article in Nature Methods was selected for the Science magazine Editor's Choice article... this week in other journals December 12, 2014.

Photo: © Flip De Nooyer/Foto Natura/Minden Pictures/Corbis 

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
Authors: Graham T Johnson, Ludovic Autin, Mostafa Al-Alusi, David S Goodsell, Michel F Sanner, & Arthur J Olson

cellPACK HIV paper

posted Dec 11, 2014, 4:46 PM by Graham Johnson   [ updated Dec 11, 2014, 5:20 PM ]

Our first applications paper, published in Faraday Discussions in September, describes how we used cellPACK to generate and test several models of mature HIV particles.
Title: 3D molecular models of whole HIV-1 virions generated with cellPACK
Abstract: As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology.
Authors: Graham T Johnson, David S Goodsell, Ludovic Autin, Stefano Forli, Michel F Sanner, & Arthur J Olson
Link:!divAbstract  The paper was published in Faraday Discussions (Royal Society of Chemistry).

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