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==Creators of Proteopedia==
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==[[Proteopedia:Overview|Overview of Proteopedia]]==
The [[Proteopedia:Overview|Overview]] '''briefly''' introduces Purpose, History, Unique Capabilities, Types of Contents, and Usage Statistics. More details follow below.


Proteopedia was created in 2007, and is maintained, by
==Proteopedia Mission Statement==
[http://www.weizmann.ac.il/home/joel/group/joel.html Joel Sussman] ([[Jls043]]),
To collect, organize and disseminate structural & functional knowledge about biomacromolecules, their assemblies and interactions with small molecules, in a user-friendly way to a broad scientific audience as a '''free, collaborative 3D-encyclopedia of proteins & other biomolecules.'''
Eran Hodis ([[EH]]),
 
and [http://bip.weizmann.ac.il/staff/jaime_prilusky.html Jaime Prilusky] ([[J_Prilusky]] or [[OCA]]).
==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.
* To foster collaborative authorship.
* To complement published articles in journals via [[I3DC|Interactive 3D Complements - '''I3DCs''']].
* To develop new '''[[Teaching strategies using Proteopedia]]'''.
 
==The Proteopedia Team==
For a gallery of the Proteopedia Team, [[Proteopedia:Team|click here]] Additional photos of Proteopedia enthusiasts are in the [[Proteopedia:Scrapbook|Scrapbook]].


==Contents of Proteopedia==
==Contents of Proteopedia==
Currently, Proteopedia has {{NUMBEROFARTICLES}} [[Special:Allpages | articles]] (pages), and {{NUMBEROFUSERS}} [[Special:Listusers | registered users]].
==Most active contributors==
<table border='1'>
<tr><td style="margin:3px; background:#D7D7FE; font-size:1.25em; font-weight:bold; border:1px solid #a3b0bf; text-align:left; color:#000; padding:0.2em 0.4em;">The Scoreboard</td></tr>
<tr><td><div id="Contribute">{{Special:ContributionScores}}Score based on pages-edited and number-of-edits.<br>List excludes members of the Proteopedia Team.<br>[[Special:ContributionScores|All scores...]]</div></td></tr>
</table>
===Seeded pages===
Proteopedia contains one page for every entry in the [http://www.wwpdb.org World Wide Protein Data Bank], which contained >148,000 entries in January, 2019. 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 code|PDB identification code]], are "seeded" automatically to include a default view of the [[Biological Unit|quaternary assembly]] ("biological unit", or if not provided by [[PDBe]], the [[asymmetric unit]]), the abstract of the publication, green links to highlight sites and ligands, and molecule-specific links to other viewers and databases. If you click "Random" in the "navigation" box at the upper left, usually you will get an article titled with a PDB code, since they outnumber human-authored articles.
===Authored pages===
In addition, there are  human-authored ''articles'' titled with the name of a molecule or a subject, instead of a PDB identification code.  In April, 2018, there were >2,900 human-authored articles. Some of these articles that have substantial content are listed at [[Proteopedia:Topic_Pages | Topic Pages]], or you can browse a [[Special:Allpages/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 [http://mediawiki.org Mediawiki], which was adapted by the Proteopedia team for macromolecular scene authoring and other special features. Proteopedia uses the [http://wiki.jmol.org/index.php/MediaWiki Jmol/JSmol Extension to MediaWiki] created by Nicolas Vervelle and adapted by the [[Proteopedia:Team|Proteopedia team]]. The [http://wiki.jmol.org/ JSmol object] is used to render the rotatable, zoomable macromolecular scenes. <!--The [http://kinemage.biochem.duke.edu/software/javamage.php MageJava] applet, by Jane and Dave Richardson is used to display kinemages.-->
==Policy==
Please see [[Proteopedia:Policy]]
==Credits==
Proteopedia was created in 2007 at the Weizmann Institute of Science by three initial [[Proteopedia:Team#Proteopedia_Founders_.26_Developers|founders and developers]]. Subsequent [[Proteopedia:Team|team members]] have helped make it what it is today.  Proteopedia is supported by [http://www.weizmann.ac.il/ISPC The Israel Structural Proteomics Center] at the [http://www.weizmann.ac.il Weizmann Institute of Science], Rehovot, Israel. [[Jmol|Jmol and JSmol]] have been made what they are today by [http://jmol.sourceforge.net/history/ many dedicated volunteers] working for many years. Notable credit goes to
[http://www.stolaf.edu/people/hansonr/ Bob Hanson], Miguel Howard, and [http://www.cac.science.ru.nl/people/egonw/ Egon Willighagen].
==Support==
* [http://www.weizmann.ac.il/icore/scb I-CORE: The Center of Research Excellence in Integrated Structural Cell Biology]
* [http://www.weizmann.ac.il/ISPC The Dana and Yossie Hollander Center for Structural Proteomics]
* [http://www.weizmann.ac.il Weizmann Institute of Science]
* [http://www.elixir-europe.org ELIXIR]
==How to cite Proteopedia==
<ref group='xtra'>doi 10.1016/j.jsb.2011.04.011</ref>
<ref group='xtra'>PMID 18673581 </ref><references group='xtra'/>
<!-- 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 [http://genomebiology.com/2008/9/8/R121 doi:10.1186/gb-2008-9-8-r121] -->
==Additional key references about Proteopedia==


Currently, Proteopedia has {{NUMBEROFARTICLES}} articles (pages), and {{NUMBEROFUSERS}} [[Special:Listusers | registered users]]. Proteopedia contains one page (or article) for every entry in the [http://www.wwpdb.org 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 and the abstract of the publication. 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).
<ref group='xtra'>Prilusky, J. & Sussman, J.L. BLOG in ''eLife'' [http://elifesciences.org/labs/a9c66d96/sharing-macromolecule-concepts-online-with-proteopedia ''Sharing macromolecule concepts online with Proteopedia'' (2016)].</ref><ref group='xtra'>doi: 10.1002/ijch.201300024</ref><ref group='xtra'>doi: 10.1007/978-94-007-2530-0_14</ref><ref group='xtra'>doi: 10.1016/j.jsb.2011.04.011</ref><ref group='xtra'>doi: 10.1002/bmb.20431</ref><ref group='xtra'>PMID 21567857 </ref><ref group='xtra'> Hodis, E., Prilusky, J., & Sussman, J.L. in From Molecules to Medicines (2009). [http://link.springer.com/chapter/10.1007/978-90-481-2339-1_11  Tools to Make 3D Structural Data More Comprehensible: Emovie & Proteopedia] pg. 169-182.</ref><ref group='xtra'>PMID 18673581 </ref><references group='xtra'/>


In addition to one article about each entry in the Protein Data Bank (PDB identification code-titled articles), there are articles about molecules or subjects.
==Contact==
If you have any questions, please contact {{Template:Contact}}.
You are also welcome to contact any of the people listed on this page. Go to their personal page, and click  "E-mail this user" in the "toolbox" at the left side of the page.
Retrieved from "https://proteopedia.org/Proteopedia:About"