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Proteopedia: A Breakthrough in Biomolecular Structure Communication

Proteopedia: A Breakthrough in Biomolecular Structure Communication. Eric Martz UMass MCB Colloquium October 27, 2008. Eran Hodis, Jaime Prilusky, Eric Martz, Joel Sussman. A Tool to Make 3D Structural Data More Comprehensible. Proteopedia. Slide adapted from Eran Hodis.

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Proteopedia: A Breakthrough in Biomolecular Structure Communication

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  1. Proteopedia: A Breakthrough in Biomolecular Structure Communication Eric Martz UMass MCB Colloquium October 27, 2008

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

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

  4. 1 2 3 4 5 6 Slide by Sussman & Hodis

  5. Levinthal and the Kluge 1965, MIT Slide by Eran Hodis

  6. Structural biology everywhere • 10 Nobel prizes since 1st protein structure solved • Covers on Nature, Science, Cell, … Slide by Eran Hodis

  7. Growth in PDB:Currently (Oct 21, 2008)53,794 structures

  8. But, structural biology still suffers from a communication problem • Often communicating 3D in 2D. • 3D is not accessible enough to non-structural biologists who 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. Slide by Eran Hodis

  9. 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 install or purchase a program. Slide by Eran Hodis

  10. Example: Lactose Repressor Wikipedia Proteopedia Both supported by Mediawiki software

  11. Proteopedia makesstructural 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 install or purchase a program. Slide by Eran Hodis

  12. PDB entry pages (seeded pages) vsprotein or protein class pages (topic pages) Dr. Jaime Prilusky Slide by Eran Hodis

  13. How easy is it to add a molecular scene? (green link) Tamiflu-resistant influenza neuraminidase N1 (3CKZ)

  14. Proteopedia makesstructural 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 install or purchase a program. Slide by Eran Hodis

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

  16. What can Proteopedia do for me? • A structure-function reference resource. • Tutorials to project in lectures and/or assign. • Journal clubs & student projects. • Supplementary materials for journal articles. • Research Group pages. Examples of each are linked to Proteopedia’s Main Page.

  17. Proteopedia differs from Wikipedia: Has Jmol(also Kinemages). Green links connect text to molecular scenes. Molecular Scene Authoring Tools.

  18. Proteopedia differs from Wikipedia: Authors’ real full names are shown on every page. Protected pages: editable only by the original author. Hidden pages to go public on publication date.

  19. A wiki for the scientific community Names of contributors are listed on each page to give credit & add accountability Slide by Eran Hodis

  20. Proteopedia http://www.proteopedia.org • Built on Open Source tools: • MediaWiki • Jmol • Content is free under GNU Free Documentation License (same as Wikipedia). • Content can be added by anyone, easily, linking text to interactive 3D.

  21. Proteopedia is already in use & evolving with feedback(over 200 registered users). How are people using it?

  22. In Journal Club: 2rd0 Fig. 2 from The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations, Huang et al. Science. 318:1744-8, 2007.

  23. Student Projects Prof. Karl Oberholser Messiah College, PA Undergrad. Student: • Emily ForscherPhotosystem II

  24. Supplementary material Crystal structure of the Agrobacterium virulence complex VirE1-VirE2 reveals a flexible protein that can accommodate different partners. Orly Dym et al. PNAS August 12, 2008 vol. 105 no. 32 11170-11175

  25. Proteopedia linked to from PSI-Nature Knowledge Base Slide by Eran Hodis

  26. In Preparation • Biological molecule vs asymmetric unit • Color by evolutionary conservation Adapted from Eran Hodis

  27. You’re invited! Proteopedia can help you with • Effective & intuitive communication of structural information • Interactive 3D supplements for journal publications • Engaging structural tutorials & lectures Without you,Proteopedia is just a tool Adapted from Eran Hodis

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

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

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