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A Tool to Make 3D Structural Data More Comprehensible

A Tool to Make 3D Structural Data More Comprehensible. Eran Hodis, Jaime Prilusky, Eric Martz, Joel Sussman. Proteopedia. Markus Fisher, Katie Rosa, Barry Honig. Thank you. It’s hard to believe, but…. 3D structures are often times hard to understand -- even for a structural biologist!.

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A Tool to Make 3D Structural Data More Comprehensible

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  1. A Tool to Make 3D Structural Data More Comprehensible Eran Hodis, Jaime Prilusky, Eric Martz, Joel Sussman Proteopedia

  2. Markus Fisher, Katie Rosa, Barry Honig Thank you

  3. It’s hard to believe, but… 3D structures are often times hard to understand -- even for a structural biologist!

  4. 1 2 3 4 5 6

  5. Levinthal and the Kluge 1965, MIT

  6. Structural biology everywhere • 13 Nobel prizes since 1st protein structure solved • Covers on Nature, Science, Cell, …

  7. Oct 7, 2008 Growth in PDB53,521 structures but…

  8. But, structural biology still suffers from a communication problem • Often communicating 3D in 2D • And not that accessible to non-structural biologists that don’t have experience with molecular visualization programs • Structural Biology, needs to make a special effort to develop tools for communication and accessibility, specifically better tools to integrate 3D structure with functional information

  9. iSee Abagyan, Lee, Raush, Budagyan,Totrov, Sundstrom & Marsden (2006) Disseminating structural genomics data to the public: from a data dump to an animated storyTIBS31 76-8

  10. Just some of the Great tools! • KING (“kinemage” kinetic image) • Protein Explorer • FirstGlance in Jmol • PDBSum • Kumar & Ziegler

  11. GOAL: to make structural information instantly accessible to a broad scientific audience 3 Key Elements: • Present 3D information in an intuitive manner • A web browser is all you need • Content can be added by anyone, easily, without need to add on/purchase a program

  12. Proteopedia aids in makingstructural information more understandable & accessible 3 Key Elements: • Present 3D information in an intuitive manner • A web browser is all you need • Content can be added by anyone, easily, without need to add on/purchase a program

  13. Lets take a look at another example poly(A) polymerase

  14. PDB entry pages (seeded pages) vsprotein or protein class pages (topic pages) Dr. Jaime Prilusky

  15. Adding scenes is easy!

  16. How easy is it to add a scene? (green link) 1acj

  17. Narrated video tutorialat Main Page www.proteopedia.org

  18. http://www.proteopedia.org Proteopedia • Built on Open Source tools: • MediaWiki • Jmol • Content is free under GNU FDL license (same as Wikipedia). Proteopedia just the vehicle for creation & dissemination • Content - can be added by anyone, easily via user friendly authoring tools to link text to 3D structures.

  19. A wiki for the scientific community • Names of contributors are listed on each page to give credit & add responsibility

  20. A wiki for the scientific community Each User can have a special area that only she/he can edit - useful for: • Tutorials • Lectures • Supplementary information for journal articles

  21. Proteopedia is already in use & evolving with feedback(over 200 registered users)

  22. How are people using it? • As a 3D encyclopedia • and…

  23. Fig. 2 2rd0 The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations., Huang CH, Mandelker D, Schmidt-Kittler O, Samuels Y, Velculescu VE, Kinzler KW, Vogelstein B, Gabelli SB, Amzel LM, Science. 2007 Dec 14;318(5857):1744-8.

  24. Assignments for class Prof. Karl Oberholser Messiah College, PA Student: • Ms. Emily ForscherPhotosystem II

  25. Supplementary material Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners Orly Dym, Shira Albeck, Tamar Unger, Jossef Jacobovitch, Anna Branzburg, Yigal Michael, Daphna Frenkiel-Krispin, Sharon Grayer Wolf, and Michael Elbaum PNAS August 12, 2008 vol. 105 no. 32 11170-11175

  26. Conformational Changes Proton Channels

  27. What to expect as a Viewing User? • Explore, but don’t expect to find a well-developed page on your favorite protein • Use the PDB entry pages to get Abstract + 3D structure on the same page

  28. Proteopedia allows you to be creative • Even though the tools are here, and the technical barriers lowered dramatically via Proteopedia’s relative ease of use … • It still takes some thought to make a good page!

  29. Proteopedia linked to from PSI-Nature Knowledge Base

  30. Coming soon • Biological molecule vs asymmetric unit • Color by evolutionary conservation • Save high resolution snapshots of 3D structures

  31. You’re invited! Proteopedia can help you with • Effective & intuitive communication of structural information • Creating 3D figures for publications • Engaging structural tutorials & lectures Without you,Proteopedia is just a tool

  32. The Proteopedia Team Dr. Jaime Prilusky Eran Hodis Prof. Joel Sussman Prof. Eric Martz Thanks also to John Moult and Israel Silman

  33. Thank you www.proteopedia.org Eran Hodis, Jaime Prilusky, Eric Martz, Israel Silman, John Moult and Joel L Sussman: Proteopedia - a scientific 'wiki' bridging the rift between 3D structure and function of biomacromolecules, Genome Biology 2008, 9:R121

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