Literature DB >> 25245078

A guide to the visual analysis and communication of biomolecular structural data.

Graham T Johnson1, Samuel Hertig2.   

Abstract

Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

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Year:  2014        PMID: 25245078     DOI: 10.1038/nrm3874

Source DB:  PubMed          Journal:  Nat Rev Mol Cell Biol        ISSN: 1471-0072            Impact factor:   94.444


  35 in total

1.  A three-dimensional model of the myoglobin molecule obtained by x-ray analysis.

Authors:  J C KENDREW; G BODO; H M DINTZIS; R G PARRISH; H WYCKOFF; D C PHILLIPS
Journal:  Nature       Date:  1958-03-08       Impact factor: 49.962

2.  Animating the model figure.

Authors:  Janet H Iwasa
Journal:  Trends Cell Biol       Date:  2010-09-09       Impact factor: 20.808

3.  Comparison of pathways from the geometric targeting method and targeted molecular dynamics in nitrogen regulatory protein C.

Authors:  Daniel W Farrell; Ming Lei; M F Thorpe
Journal:  Phys Biol       Date:  2011-04-06       Impact factor: 2.583

4.  Points of view: Avoiding color.

Authors:  Bang Wong
Journal:  Nat Methods       Date:  2011-07       Impact factor: 28.547

5.  Pencil and paper.

Authors:  Bang Wong; Rikke Schmidt Kjægaard
Journal:  Nat Methods       Date:  2012-11       Impact factor: 28.547

6.  Biochemistry. Integrative structural biology.

Authors:  Andrew B Ward; Andrej Sali; Ian A Wilson
Journal:  Science       Date:  2013-02-22       Impact factor: 47.728

7.  ePMV embeds molecular modeling into professional animation software environments.

Authors:  Graham T Johnson; Ludovic Autin; David S Goodsell; Michel F Sanner; Arthur J Olson
Journal:  Structure       Date:  2011-03-09       Impact factor: 5.006

8.  An introduction to biomolecular graphics.

Authors:  Cameron Mura; Colin M McCrimmon; Jason Vertrees; Michael R Sawaya
Journal:  PLoS Comput Biol       Date:  2010-08-26       Impact factor: 4.475

9.  Divergent evolution of protein conformational dynamics in dihydrofolate reductase.

Authors:  Gira Bhabha; Damian C Ekiert; Madeleine Jennewein; Christian M Zmasek; Lisa M Tuttle; Gerard Kroon; H Jane Dyson; Adam Godzik; Ian A Wilson; Peter E Wright
Journal:  Nat Struct Mol Biol       Date:  2013-09-29       Impact factor: 15.369

10.  Game on, science - how video game technology may help biologists tackle visualization challenges.

Authors:  Zhihan Lv; Alex Tek; Franck Da Silva; Charly Empereur-mot; Matthieu Chavent; Marc Baaden
Journal:  PLoS One       Date:  2013-03-06       Impact factor: 3.240

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  13 in total

1.  Creating Stop-Motion Animations to Learn Molecular Biology Dynamics.

Authors:  Celeste N Peterson; Pauline Ngo
Journal:  J Microbiol Biol Educ       Date:  2015-12-01

2.  Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.

Authors:  Samuel Hertig; Thomas D Goddard; Graham T Johnson; Thomas E Ferrin
Journal:  Biophys J       Date:  2015-05-05       Impact factor: 4.033

3.  The Scientist as Illustrator.

Authors:  Janet H Iwasa
Journal:  Trends Immunol       Date:  2016-03-09       Impact factor: 16.687

4.  Structure of cell-cell adhesion mediated by the Down syndrome cell adhesion molecule.

Authors:  Luqiang Guo; Yichun Wu; Haishuang Chang; Ze Zhang; Hua Tang; Yang Yu; Lihui Xin; Yingbin Liu; Yongning He
Journal:  Proc Natl Acad Sci U S A       Date:  2021-09-28       Impact factor: 11.205

5.  Instant Construction and Visualization of Crowded Biological Environments.

Authors:  Tobias Klein; Ludovic Autin; Barbora Kozlikova; David S Goodsell; Arthur Olson; M Eduard Groller; Ivan Viola
Journal:  IEEE Trans Vis Comput Graph       Date:  2017-08-29       Impact factor: 4.579

Review 6.  Molecular Illustration in Research and Education: Past, Present, and Future.

Authors:  David S Goodsell; Jodie Jenkinson
Journal:  J Mol Biol       Date:  2018-05-09       Impact factor: 5.469

Review 7.  Quantifying Modes of 3D Cell Migration.

Authors:  Meghan K Driscoll; Gaudenz Danuser
Journal:  Trends Cell Biol       Date:  2015-10-23       Impact factor: 20.808

8.  BlendMol: advanced macromolecular visualization in Blender.

Authors:  Jacob D Durrant
Journal:  Bioinformatics       Date:  2019-07-01       Impact factor: 6.937

9.  SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information.

Authors:  Syed S Husain; Alexandr Kalinin; Anh Truong; Ivo D Dinov
Journal:  J Big Data       Date:  2015

10.  Elfin UI: A Graphical Interface for Protein Design With Modular Building Blocks.

Authors:  Chun-Ting Yeh; Leon Obendorf; Fabio Parmeggiani
Journal:  Front Bioeng Biotechnol       Date:  2020-10-23
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