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

Narrated video tutorialat Main Page

www.proteopedia.org

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