Skip to main content

Tools to Make 3D Structural Data More Comprehensible: Emovie & Proteopedia

  • Conference paper
Book cover From Molecules to Medicines

Abstract

To the crystallographer, solving a three-dimensional (3D) protein or molecular structure often times feels like the ultimate success, and surely it is. However, of utmost importance is the communication of the insights revealed by the 3D structure, especially those insights that relate structure to function. In order for these insights to reach their potential for guiding future research, they must reach biologists. The problem is that 3D structures are inherently complex and thus communicating insights about 3D structures to non-structural biologists can be difficult. To aid the structural biologist in this endeavor, we have created two useful tools. The first, eMovie, is a plug- in for PyMOL that makes creating macromolecular animations much more simple. The second, Proteopedia, is a community-annotated ‘wiki’ web- resource that links descriptive text to 3D views of structures, resulting in intuitive communication of structural information.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Hodis, E., Schreiber, G., Rother, K. & Sussman, J. L., eMovie: A storyboard-based tool for making molecular movies, TIBS 32, 199–204 (2007).

    Google Scholar 

  2. Hodis, E., Prilusky, J., Martz, E., Silman, I., Moult, J. & Sussman, J. L., Proteopedia -a scientific ‘wiki’ bridging the rift between three-dimensional structure and function of biomacromolecules, Genome Biol. 9, R121 (2008).

    Article  Google Scholar 

  3. Levinthal, C., Molecular model-building by computer, Sci. Am. 214, 42–52 (1966).

    Article  Google Scholar 

  4. Richardson, D. C. & Richardson, J. S., The kinemage: A tool for scientific communication, Protein Sci. 1, 3–9 (1992).

    Article  Google Scholar 

  5. Sayle, R. A. & Milner-White, E. J., RASMOL: biomolecular graphics for all, TIBS 20, 374–376 (1995).

    Google Scholar 

  6. Stampf, D. R., Felder, C. E. & Sussman, J. L., PDBBrowse - a graphics interface to the Brookhaven protein data bank, Nature 374, 572–574 (1995).

    Article  ADS  Google Scholar 

  7. Peitsch, M. C., Stampf, D. R., Wells, T. N. C. & Sussman, J. L., The Swiss 3D-Image collection and Brookhaven protein data bank browser on the World-Wide Web, TIBS 20, 82–84 (1995).

    Google Scholar 

  8. Abagyan, R., Lee, W. H., Raush, E., Budagyan, L., Totrov, M., Sundstrom, M. & Marsden, B. D., Disseminating structural genomics data to the public: From a data dump to an animated story, TIBS 31, 76–78 (2006).

    Google Scholar 

  9. Jmol.

    Google Scholar 

  10. Wikipedia.

    Google Scholar 

  11. MediaWiki.

    Google Scholar 

  12. Vervelle, N. Jmol MediaWiki Extension.

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science + Business Media B.V.

About this paper

Cite this paper

Hodis, E., Prilusky, J., Sussman, J.L. (2009). Tools to Make 3D Structural Data More Comprehensible: Emovie & Proteopedia. In: Sussman, J.L., Spadon, P. (eds) From Molecules to Medicines. NATO Science for Peace and Security Series A: Chemistry and Biology. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2339-1_11

Download citation

Publish with us

Policies and ethics