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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

A Tool to Make 3D Structural Data More Comprehensible

Eran Hodis,

Jaime Prilusky,

Eric Martz,

Joel Sussman

Proteopedia

it s hard to believe but
It’s hard to believe, but…

3D structures are often times hard to understand -- even for a structural biologist!

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structural biology everywhere
Structural biology everywhere
  • 13 Nobel prizes since 1st protein structure solved
  • Covers on Nature, Science, Cell, …
but structural biology still suffers from a communication problem
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
slide9
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

just some of the great tools
Just some of the Great tools!
  • KING (“kinemage” kinetic image)
  • Protein Explorer
  • FirstGlance in Jmol
  • PDBSum
  • Kumar & Ziegler
goal to make structural information instantly accessible to a broad scientific audience
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
proteopedia aids in making structural information more understandable accessible
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
pdb entry pages seeded pages vs protein or protein class pages topic pages
PDB entry pages (seeded pages) vsprotein or protein class pages (topic pages)

Dr. Jaime Prilusky

proteopedia

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.
a wiki for the scientific community
A wiki for the scientific community
  • Names of contributors are listed on each page to give credit & add responsibility
a wiki for the scientific community1
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
how are people using it
How are people using it?
  • As a 3D encyclopedia
  • and…
fig 2
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.

assignments for class
Assignments for class

Prof. Karl Oberholser

Messiah College, PA

Student:

  • Ms. Emily ForscherPhotosystem II
supplementary material
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

conformational changes
Conformational Changes

Proton Channels

what to expect as a viewing user
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
proteopedia allows you to be creative
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!
proteopedia linked to from
Proteopedia linked to from

PSI-Nature Knowledge Base

coming soon
Coming soon
  • Biological molecule vs asymmetric unit
  • Color by evolutionary conservation
  • Save high resolution snapshots of 3D structures
you re invited
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

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The Proteopedia Team

Dr. Jaime Prilusky

Eran Hodis

Prof. Joel Sussman

Prof. Eric Martz

Thanks also to John Moult and Israel Silman

thank you
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