Proteopedia:About

From Proteopedia

Revision as of 16:49, 26 September 2010

Proteopedia Mission Statement

To collect, organize and disseminate structural and functional knowledge about protein, RNA, DNA, and other macromolecules, and their assemblies and interactions with small molecules, in a manner that is relevant and broadly accessible to students and scientists.

Goals for Proteopedia

• To serve as a forum for the scientific community to share, retrieve and discuss information related to proteins, macromolecules, and small molecules and chemicals of interest.
• To continue to develop the concept of tying text to three-dimensional, interactive images.
• To maintain low barriers for contribution.

The Proteopedia Team

Proteopedia Founders & Developers

Jaime Prilusky Co-Founder

Eran Hodis Co-Founder

Joel Sussman Co-Founder

Proteopedia Editorial Board

Karl Oberholser Editor

Wayne Decatur Editor

Proteopedia Advisory Board

Eric Martz Advisor, Collaborator

Israel Silman Advisor

John Moult Advisor

Proteopedia I3DC Board

Jaime Prilusky Scientific Editor

David Canner Scientific Artist

How to cite Proteopedia

• Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121

Contents of Proteopedia

Currently, Proteopedia has 271,490 articles (pages), and 5,911 registered users. Among other pages, Proteopedia contains one page (or article) for every entry in the World Wide Protein Data Bank. Proteopedia is updated weekly with new entries shortly after they are released by the Protein Data Bank. Most of these pages, which are titled with a four-character PDB identification code, are "seeded" automatically to include a default view of the asymmetric unit, the abstract of the publication, green links to sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random page, you nearly always get one of these automatically-seeded, PDB-code-titled pages (click Random Page in the navigation box at the upper left), because of their abundance.

In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles titled with the name of a molecule or a subject, instead of a PDB identification code. Some of these articles that have substantial content are listed at Topic Pages, or you can browse a complete list of articles not titled with a PDB identification code. There are also articles About Macromolecular Structure.

Wishlist and Problems

Please list desired new features on the page Proteopedia:Wishlist and problems you have encountered on the page Proteopedia:Problems.

Email List

You are invited to subscribe to the Proteopedia:Email list in order to receive announcements of new features or pages in Proteopedia. It is also the central forum to ask for help or discuss proposals for new capabilities.

Implementation

Proteopedia was built with Mediawiki, which was adapted by the Proteopedia team for macromolecular scene authoring and other special features. Proteopedia uses the Jmol Extension to MediaWiki created by Nicolas Vervelle and adapted by the Proteopedia team. The Jmol java applet is used to render the rotatable, zoomable macromolecular scenes. The MageJava applet, by Jane and Dave Richardson is used to display kinemages.

Credits

Proteopedia was created in 2007 at the Weizmann Institute of Science. Proteopedia is supported by The Israel Structural Proteomics Center at the Weizmann Institute of Science, Rehovot, Israel. Jmol has been made what it is today by many dedicated volunteers working for many years. Notable credit goes to Bob Hanson, Miguel Howard, and Egon Willighagen.

Contact

If you have any questions, please contact . You are also welcome to contact any of the people listed on this page. Their email addresses are on their personal pages.