Proteopedia:About

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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.

Policy

Please see Proteopedia:Policy

The Proteopedia Team

For a gallery of the Proteopedia Team, click here

How to cite Proteopedia

  • Prilusky J, Hodis E, Canner D, Decatur W, Oberholser K, Martz E, Berchanski A, Harel M, Sussman JL. Proteopedia: A status report on the collaborative, 3D web-encyclopedia of proteins and other biomolecules. J Struct Biol. 2011 Apr 23. PMID:21536137 doi:10.1016/j.jsb.2011.04.011
  • 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 136,972 articles (pages), and 3,488 registered users. Among others, Proteopedia contains one page 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 highlight sites and ligands, and molecule-specific links to other viewers and databases. When you go to a random PDB entry, you will get one of these automatically-seeded, PDB-code-titled pages (click Random PDB entry in the random box at the upper left).

In addition to one machine-generated page about each entry in the Protein Data Bank (PDB identification code-titled pages), there are human-authored 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. If you click "Random article" in the "random" box at the upper left, you will get one of these human-authored articles.

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 by three initial founders and developers. Subsequent team members have helped make it what it is today. 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.

Support

Contact

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

Proteopedia Page Contributors and Editors (what is this?)

Eran Hodis, Eric Martz, Jaime Prilusky, Joel L. Sussman, Wayne Decatur, David Canner

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