A Tool to Make 3D Structural Data More Comprehensible
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Transcript of A Tool to Make 3D Structural Data More Comprehensible
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ProteopediaProteopedia
Eran Hodis, Jaime Prilusky,
Eric Martz,Joel Sussman
A Tool to Make 3D Structural Data More Comprehensible
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Markus Fisher, Katie Rosa, Barry Honig
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Thank you
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It’s hard to believe, but…
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3D structures are often times hard to understand -- even for a structural biologist!
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Levinthal and the Kluge
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1965, MIT
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Structural biology everywhere
• 13 Nobel prizes since 1st protein structure solved
• Covers on Nature, Science, Cell, …
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'72 '75 '78 '81 '84 '87 '90 '93 '96 '99 '02 '05 '08
Growth in PDBGrowth in PDB53,521 53,521
structuresstructures
but…
Oct 7, 2008
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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
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iSee
Abagyan, Lee, Raush, Budagyan,Totrov, Sundstrom & Marsden (2006) Disseminating structural genomics data to the public: from a data dump to an animated story TIBS 31 76-8
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Just some of the Great tools!
• KING (“kinemage” kinetic image)• Protein Explorer• FirstGlance in Jmol• PDBSum• Kumar & Ziegler
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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
GOAL: to make structural information instantly accessible to a broad
scientific audience
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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
Proteopedia aids in makingstructural information
more understandable & accessible
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Lets take a look at another example
poly(A) polymerase
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PDB entry pages (seeded pages) vs
protein or protein class pages (topic pages)
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Dr. Jaime Prilusky
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Adding scenes is easy!
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How easy is it to add a scene? (green link)
1acj
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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.
http://www.proteopedia.org
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A wiki for the scientific community
• Names of contributors are listed on each page to give credit & add responsibility
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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
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Proteopedia is already in use & evolving with feedback
(over 200 registered users)
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How are people using it?
• As a 3D encyclopedia• and…
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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.
2rd0Fig. 2
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Assignments for class
Prof. Karl OberholserMessiah College, PAStudent:• Ms. Emily Forscher
Photosystem II
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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
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Conformational Changes
Proton Channels
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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
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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!
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Proteopedia linked to from
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PSI-Nature Knowledge Base
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Coming soon
• Biological molecule vs asymmetric unit
• Color by evolutionary conservation• Save high resolution snapshots of
3D structures
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You’re invited!
Proteopedia can help you with
1) Effective & intuitive communication of structural information
2) Creating 3D figures for publications
3) Engaging structural tutorials & lectures
Without you, Proteopedia is just a
tool
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The Proteopedia Team
Thanks also to John Moult and Israel Silman
Prof. Joel Sussman
Dr. Jaime Prilusky Eran
Hodis
Prof. Eric Martz
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Thank you
www.proteopedia.orgEran 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