Proteopedia: A Breakthrough in Biomolecular Structure Communication Eric Martz UMass MCB Colloquium October 27, 2008

Proteopedia 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

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

Growth in PDB: Currently (Oct 21, 2008) 53,794 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

WikipediaProteopedia 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 makes structural information more understandable & accessible: Slide by Eran Hodis

PDB entry pages (seeded pages) vs protein or protein class pages (topic pages)seeded pages Dr. Jaime Prilusky Slide 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 makes structural information more understandable & accessible: Slide by Eran Hodis

Narrated video tutorial at Main Page

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.

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, rd0 In Journal Club:

Student Projects Prof. Karl Oberholser Messiah College, PA Undergrad. 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

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 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

A wiki for the scientific community Each User has a special area that only she/he can edit for: Tutorials Lecture Illustrations Supplementary materials for journal articles Slide by Eran Hodis

Let’s take a look at another example poly(A) polymerase Slide by Eran HodisImage by David Goodsell

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