Proteopedia:About

From Proteopedia

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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.

The Proteopedia Team

Jaime Prilusky Co-Founder	Eran Hodis Co-Founder	Joel Sussman Co-Founder
No foto.png Israel Silman Advisor	No foto.png John Moult Advisor	Eric Apr08.png Eric Martz Editor

How to cite Proteopedia

Eran 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 doi:10.1186/gb-2008-9-8-r121

Contents of Proteopedia

Currently, Proteopedia has 271,490 articles (pages), and 5,913 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.

Proteopedia in the News

Read about Proteopedia in the news at Proteopedia:News

Wishlist and Problems

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

Page Contributors, Content Donators, and Editors

For an explanation of the distinctions between these types of contributors, please see Proteopedia Page Contributors and Editors.

License Information

For license information see Proteopedia:Terms_of_Service

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.

Namespace Pages

Namespaces

In addition to its regular articles (which represent the vast majority of its content), Proteopedia contains articles grouped in subsections called namespaces. Namespaces appear as the first word in the title of a page, followed by a colon. For example, this page Proteopedia:Namespaces is in the namespace Proteopedia:. Namespaces are formal regions within the wiki that are assigned by administrators.

Non-Namespaces Simply using a colon in the title of a page does not create a new namespace. For example, these pages are not in namespaces: Acetylcholinesterase: Substrate Traffic and Inhibition Treatments:Hypertension.

Searches can be restricted to a subset of namespaces. After any search, you can see a list of namespaces, with checkboxes, at the bottom of the result page. Your preferences control which namespaces are searched, by default, for your login. However, by checking or unchecking the namespaces at the bottom of any search result, and then clicking on the Search button near the list of namespaces, you can re-run the search for any specified subset of namespaces.

Proteopedia includes the following namespaces. You can display all pages within one of these namespaces by clicking on the link below.

• Users: All user pages with content or the list of all registered users.

• Proteopedia: includes About, Namespaces, Policy, Troubleshooting, Problems, Wishlist, and Topic Pages.

• Image: includes all files that have been uploaded to Proteopedia.

• Mediawiki: includes technical support pages.

• Template: includes all templates (there are many!). A template is generally some wikitext content that is designed to be included in other pages.

• Help: includes help pages that were created within the Help namespace.

• Category: All category pages with content or the list of all automatically-generated categories.

• Journal: includes pages belonging to specific journals.

• Tutorial: includes High School tutorials .

The above list is incomplete. A complete list of all namespaces in Proteopedia is displayed in the list of checkboxes at the very bottom of search results. See also Help:Searching.

Subdirectories

Subdirectories end with a slash ("/") instead of a colon. Please see Proteopedia:Subdirectories.

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, and is maintained, by Joel L. Sussman (User:Joel_L._Sussman), Eran Hodis (User:Eran_Hodis), and Jaime Prilusky (User:Jaime_Prilusky).

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 under Credits above. Their email addresses are on their personal pages.