Proteopedia: A Breakthrough in
Biomolecular Structure
Communication
Eric Martz
UMass MCB Colloquium
October 27, 2008
ProteopediaProteopedia
Eran Hodis, Jaime Prilusky,Eric Martz,Joel Sussman
A Tool to Make 3D Structural Data More Comprehensible
Slide adapted from Eran Hodis
It’s hard to believe, but…
3D structures are often times hard to understand -- even for a structural biologist!
Slide by Eran Hodis
1 2 3
4 5 6
Slide by Sussman & Hodis
Levinthal and the Kluge
1965, MIT
Slide by Eran Hodis
Structural biology everywhere
• 10 Nobel prizes since 1st protein structure solved
• Covers on Nature, Science, Cell, …
Slide by Eran Hodis
'72 '75 '78 '81 '84 '87 '90 '93 '96 '99 '02 '05 '08
Growth in PDB:Growth in PDB:Currently (Oct 21, Currently (Oct 21,
2008)2008)53,794 structures53,794 structures
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
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.
GOAL: to make structural information instantly accessible to a broad
scientific audience
Slide by Eran Hodis
Wikipedia Proteopedia
Both supported by Mediawiki software
Example: Lactose Repressor
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.
Proteopedia makesstructural information
more understandable & accessible:
Slide by Eran Hodis
PDB entry pages (seeded pages) vs
protein or protein class pages (topic pages)
Dr. Jaime PriluskySlide by Eran Hodis
How easy is it to add a molecular scene? (green link)
Tamiflu-resistant influenza neuraminidase N1 (3CKZ)
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.
Proteopedia makesstructural information
more understandable & accessible:
Slide by Eran Hodis
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.
Proteopedia differs from Wikipedia:
1. Has Jmol (also Kinemages).
2. Green links connect text to molecular scenes.
3. Molecular Scene Authoring Tools.
Proteopedia differs from Wikipedia:
4. Authors’ real full names are shown on every page.
5. Protected pages: editable only by the original author.
6. Hidden pages to go public on publication date.
A wiki for the scientific community
Names of contributors are listed on each page to give credit & add accountability
Slide by Eran Hodis
Proteopedia
• 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.
http://www.proteopedia.org
Proteopedia is already in use & evolving with feedback
(over 200 registered users).
How are people using it?
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.
2rd0
In Journal Club:
Student Projects
Prof. Karl OberholserMessiah College, PAUndergrad. Student:• Emily Forscher
Photosystem II
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
Proteopedia linked to from
PSI-Nature Knowledge Base
Slide by Eran Hodis
In Preparation
• Biological molecule vs asymmetric unit
• Color by evolutionary conservation
Adapted from Eran Hodis
You’re invited!
Proteopedia can help you with
1) Effective & intuitive communication of structural information
2) Interactive 3D supplements for journal publications
3) Engaging structural tutorials & lectures
Without you, Proteopedia is just a tool
Adapted from Eran Hodis
The Proteopedia Team
Thanks also to John Moult and Israel Silman
Joel Sussman
Jaime Prilusky Eran
Hodis
Eric Martz
Thank you
www.proteopedia.org
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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