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

Nature Reviews Molecular Cell Biology

Volumn 15, Issue 10, 2014, Pages 690-698

  Johnson, Graham T ^a,b,c   Hertig, Samuel ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CHEMICAL STRUCTURE; COMPUTER PROGRAM; DATA ANALYSIS; INTERPERSONAL COMMUNICATION; PRIORITY JOURNAL; REVIEW; SCIENTIST; STRUCTURE ANALYSIS; VISUAL INFORMATION; ARTICLE; INFORMATION DISSEMINATION; PROTEIN CONFORMATION; PROTEIN DATABASE; PUBLISHING;

DATABASES, PROTEIN; INFORMATION DISSEMINATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PUBLISHING;

EID: 84908106416     PISSN: 14710072     EISSN: 14710080     Source Type: Journal    
DOI: 10.1038/nrm3874     Document Type: Review

References (51)

1. Kendrew, J. C. et al. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181, 662-666 (1958
2. Zhao, G. et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-Atom molecular dynamics. Nature 497, 643-646 (2013
3. Takamori, S. et al. Molecular anatomy of a trafficking organelle. Cell 127, 831-846 (2006
4. Wilhelm, B. G. et al. Composition of isolated synaptic boutons reveals the amounts of vesicle trafficking proteins. Science 344, 1023-1028 (2014
5. Johnson, G. et al. 3D molecular models of whole HIV-1 virions generated with cellPACK. Faraday Discuss. (in the press
6. Ward, A. B., Sali, A., & Wilson, I. A. Biochemistry. Integrative structural biology. Science 339, 913-915 (2013
7. Iwasa, J. H. Animating the model figure. Trends Cell Biol. 20, 699-704 (2010
8. McGill, G. Molecular movies⋯ coming to a lecture near you. Cell 133, 1127-1132 (2008
9. Johnson, G. T., Autin, L., Goodsell, D. S., Sanner, M. F., & Olson, A. J. ePMV embeds molecular modeling into professional animation software environments. Structure 19, 293-303 (2011
10. Autin, L., Johnson, G., Hake, J., Olson, A., & Sanner, M. uPy: a ubiquitous CG Python API with biological-modeling applications. IEEE Computer Graph. Appl. 32, 50-61 (2012
11. Goodsell, D. S., & Johnson, G. T. Filling in the gaps: artistic license in education and outreach. PLoS Biol. 5, e308 (2007
12. Wong, B., & Kjaegaard, R. S. Pencil and paper. Nature Methods 9, 1037 (2012
13. Kozma, D., Simon, I., & Tusnády, G. E. PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res. 41, D524-D529 (2013
14. Lomize, M. A., Lomize, A. L., Pogozheva, I. D., & Mosberg, H. I. OPM: orientations of proteins in membranes database. Bioinformatics 22, 623-625 (2006
15. Rundgren, C. J., & Tibell, L. A. E. Critical features of visualizations of transport through the cell membrane - an empirical study of upper secondary and tertiary students' meaning-making of a still image and an animation. Int. J. Sci. Math. Educ. 8, 223-246 (2010
16. Kramer, I. M., Dahmani, H. R., Delouche, P., Bidabe, M., & Schneeberger, P. Education catching up with science: preparing students for three-dimensional literacy in cell biology. CBE Life Sci. Educ. 11, 437-447 (2012
17. O'Donoghue, S. I. et al. Visualizing biological data - now and in the future. Nature Methods 7, S2-S4 (2010
18. O'Donoghue, S. I. et al. Visualization of macromolecular structures. Nature Methods 7, S42-S55 (2010
19. Hornus, S., Levy, B., Lariviere, D., & Fourmentin, E. Easy DNA modeling and more with GraphiteLifeExplorer. PLoS ONE 8, e53609 (2013
20. Kremer, J. R., Mastronarde, D. N., & McIntosh, J. R. Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116, 71-76 (1996
21. Walter, T. et al. Visualization of image data from cells to organisms. Nature Methods 7, S26-S41 (2010
22. Pettersen, E. F. et al. UCSF chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004
23. Hanson, R. M. Jmol - a paradigm shift in crystallographic visualization. J. Appl. Crystallogr. 43, 1250-1260 (2010
24. Sanner, M. F. Python: a programming language for software integration and development. J. Mol. Graph. Model. 17, 57-61 (1999
25. DeLano, W. L. The PyMOL molecular graphics system. DeLano Scientific [online], http://www.pymol.org (2002
26. Humphrey, W., Dalke, a., & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33-38, 27-28 (1996
27. Alberts, B. et al. Molecular Biology of the Cell 4th edn (Garland Science, 2002
28. Pollard, T. D., Earnshaw, W., & Lippincott-Schwartz, J. Cell Biology 2nd edn Ch. 27 (Elsevier, 2007
29. Iwasa, J. H., & Johnson, G. The art and science of cell biology (ASCB2). ASCB Newsletter 35, 3-5 (2012
30. Johnson, G. T. Announcing the Winners of the autoPACK visualization Challenge2012: present HIV in blood plasma. AMI Newsletter (AMI, 2013
31. Johnson, G. T. Interview iwth Drew Berry, 2010 MacArther Fellow. AMI Newsletter (Association of Medical Illustrators, 2011
32. Berry, D. Molecular animation of cell death mediated by the fas pathway. Sci. STKE 2007, tr1 (2007
33. Downey, A. Think Python (O'Reilly Media, 2012
34. Lv, Z. et al. Game on, science - how video game technology may help biologists tackle visualization challenges. PLoS ONE 8, e57990 (2013
35. Johnson, G. T. et al. cellPACK: a virtual mesoscope to model and visualize structural systems biology. Nature Methods (in the press
36. Bhabha, G. et al. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nature Struct. Mol. Biol. 20, 1243-1249 (2013
37. Tarini, M., Cignoni, P., & Montani, C. Ambient occlusion and edge cueing to enhance real time molecular visualization. IEEE Computer Graph. Appl. 11, 1237-1244 (2006
38. Krebs, W. G., & Gerstein, M. The morph server: a standardized system for analyzing and visualizing macromolecular motions in a database framework. Nucleic Acids Res. 28, 1665-1675 (2000
39. Farrell, D. W., Lei, M., & Thorpe, M. F. Comparison of pathways from the geometric targeting method and targeted molecular dynamics in nitrogen regulatory protein C. Phys. Biol. 8, 026017 (2011
40. Tufte, E. R. Envisioning information. Optom. Vision Sci. 68, 322-324 (1991
41. Tufte, E. R., & Graves-Morris, P. The Visual Display of Quantitative Information (Graphics Press Cheshire, 1983
42. Wong, B. Points of view: color coding. Nature Methods 7, 573-573 (2010
43. Wong, B. Points of view: color blindness. Nature Methods 8, 441-441 (2011
44. Wong, B. Points of view: avoiding color. Nature Methods 8, 525-525 (2011
45. McCloud, S. Understanding Comics: the Invisible Art (Tundra Pub., 1993
46. McGill, G. Protein dynamics. EMBL Conference on Visualizing Biological Data [online], http://vizbi.org/Videos/26199717 (2011
47. Miko, I. Episode 19: HMS's Gael McGill on molecular visualization. Nature Education [online], http://www.nature.com/scitable/blog/natureedcast/episode-19-hmss-gael-mcgill (2011
48. Vale, R. D., & Milligan, R. A. The way things move: looking under the hood of molecular motor proteins. Science 288, 88-95 (2000
49. Carter, A. P., Cho, C., Jin, L., & Vale, R. D. Crystal structure of the dynein motor domain. Science 331, 1159-1165 (2011
50. Pollard, T.D., Earnshaw, W. C., & Johnson, G. T. Electronic Image Collection for Cell Biology (W. B. Saunders, 2002
51. Mura, C., McCrimmon, C. M., Vertrees, J., & Sawaya, M. R. An introduction to biomolecular graphics. PLoS Comput. Biol. 6, e1000918 (2010).