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

ProteopediaProteopedia

Eran Hodis, Jaime Prilusky,

Eric Martz,Joel Sussman

A Tool to Make 3D Structural Data More Comprehensible

Markus Fisher, Katie Rosa, Barry Honig

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Thank you

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





1965, MIT

Structural biology everywhere

• 13 Nobel prizes since 1st protein structure solved

• Covers on Nature, Science, Cell, …

'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

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



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

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

http://www.proteopedia.org/wiki/index.php/Hemoglobin

http://en.wikipedia.org/wiki/Hemoglobin

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

Lets take a look at another example

poly(A) polymerase



PDB entry pages (seeded pages) vs

protein or protein class pages (topic pages)



Dr. Jaime Prilusky

Adding scenes is easy!

How easy is it to add a scene? (green link)

1acj

Narrated video tutorialat Main Page

www.proteopedia.org

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.

http://www.proteopedia.org

A wiki for the scientific community

• Names of contributors are listed on each page to give credit & add responsibility

http://proteopedia.org/wiki/index.php/Main_Page

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

http://proteopedia.org/wiki/index.php/Main_Page

Proteopedia is already in use & evolving with feedback

(over 200 registered users)

How are people using it?

• As a 3D encyclopedia• and…



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

Assignments for class

Prof. Karl OberholserMessiah College, PAStudent:• Ms. 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, 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

Proton Channels





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

• 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





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









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

The Proteopedia Team

Thanks also to John Moult and Israel Silman

Prof. Joel Sussman

Dr. Jaime Prilusky Eran

Hodis

Prof. Eric Martz

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

http://www.proteopedia.org/wiki/index.php/Hemoglobin

Documents

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