Publications

Software

Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. autoPACK. LGPL open-source, autoPACK.org, UCSF and The Scripps Research Institute, 2006–2013.

Johnson G, Autin L, Al-Alusi M, Goodsell D, Sanner M, Olson A. cellPACK. LGPL open-source, autoPACK.org, UCSF and The Scripps Research Institute, 2006–2013.

Autin L, Johnson G, Sanner M, Olson A. Ubiquitous Python API (uPy). LGPL open-source, The Scripps Research Institute, 2012.

Autin L and Johnson G, Sanner M, Olson A. Embedded Python Molecular Viewer (ePMV). LGPL open-source, The Scripps Research Institute, 2010.


Peer Reviewed Publications

Johnson GT, Autin L, Al-Alusi M, Goodsell DS, Sanner MF, Olson AJ. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nat Methods. 2015 Jan; 12(1):85-91. PMID: 25437435. PMCID: PMC4281296 DOI: 10.1038/nmeth.3204

Sali, A. et al. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure (2015).

Johnson, G.T. & Hertig, S. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev Mol Cell Biol 15, 690-8 (2014). doi:10.1038/nrm3874

Johnson, G.T., Goodsell, D. S., Autin, L., Forli, S., Sanner, M.F., Olson, A.J. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discussions (2014), doi:10.1039/C4FD00017J.


Hertig, S., Goddard, T.D., Johnson, G.T. & Ferrin, T.E. Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins. Biophys J 108, 2097-102 (2015).

Autin L, Johnson G, Hake J, Olson A, Sanner M, uPy: A Ubiquitous CG Python API with Biological-Modeling Applications, IEEE Computer Graphics and Applications, vol. 32, no. 5, pp. 50-61, Sept.-Oct. 2012, doi:10.1109/MCG.2012.93

Johnson, G.T., Autin, L., Goodsell, D.S., Sanner, M.F., Olson, A.J. (2011). ePMV Embeds Molecular Modeling into Professional Animation Software Environments. Structure 19, 293-303.

Al-Amoudi, A., Castaño-Diez, D., Devos, D. P., Russell, R. B., Johnson, G.T., Frangakis, A.S. (2011). The three- dimensional molecular structure of the desmosomal plaque. PLoS Biol 5, e308.

Goodsell, D.S., and Johnson, G.T. (2007). Filling in the gaps: artistic license in education and outreach. PLoS Biol 5, e308.


Non Peer Reviewed Publications

Johnson, G. (2013) AMI Newsletter: Announcing the Winners of the autoPACK Visualization Challenge2012: Present HIV in Blood Plasma. (Lexington: AMI). 

Johnson, G., de Kok-Mercado, F., Autin, L. (2012) AMI Newsletter: ePMV embedded Python Molecular Viewer. (Lexington: AMI). 

Johnson, G. (2011) AMI Newsletter: Interview with Drew Berry, 2010 MacArthur Fellow. (Lexington: AMI).

Written Interview Response: Goodsell, D. S. (2009). RCSB Protein Data Bank Newsletter 41, PDB Community Focus: Gael McGill, Ph.D., and Graham Johnson, Molecular Animators. (Piscataway: RCSB).

Johnson, G. T., Goodsell, D. S.. Molecule of the Month: Clathrin. Protein Data Bank, www.rcsb.org, (2007). 

Co-authored as Illustrator: T Pollard, W Earnshaw, J Lippincott-Schwartz. Cell Biology 2e. Elsevier, NY, 2007.

Co-authored as Illustrator: Pollard T, Earnshaw W, Lippincott-Schwartz J. Cell Biology 1e. Elsevier, NY, 2002.


Interviews, uses, mentions

http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2223.html

Subpages (1): NRMCB
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