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===Proteopedia Mission Statement===
__TOC__
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.
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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.


===Goals for Proteopedia===
==Proteopedia Mission Statement==
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.'''
 
==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 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 continue to develop the concept of tying text to three-dimensional, interactive images.
* To maintain low barriers for contribution.
* 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==
==The Proteopedia Team==
<gallery perrow="3">
For a gallery of the Proteopedia Team, [[Proteopedia:Team|click here]] Additional photos of Proteopedia enthusiasts are in the [[Proteopedia:Scrapbook|Scrapbook]].
Image:J_Prilusky.jpg|[[User:Jaime_Prilusky|Jaime Prilusky]]<br>'''Co-Founder'''
Image:Eran_hodis_cropped.png|[[User:Eran_Hodis|Eran Hodis]]<br>'''Co-Founder'''
Image:Joel_Sussman_2.jpg|[[User:Joel_L._Sussman|Joel Sussman]]<br>'''Co-Founder'''
</gallery>
 
==Proteopedia Advisory Board==
<gallery perrow="3">
Image:Eric Martz.jpg|[[User:Eric_Martz|Eric Martz]]<br>'''Advisor, Editor'''
Image:Israel Silman.jpg|Israel Silman<br>'''Advisor'''
Image:John moult.png|John Moult<br>'''Advisor'''
</gallery>
 
==Proteopedia Editorial Board==
Proteopedia is in the process of forming an Editorial Board.
 
==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 [http://genomebiology.com/2008/9/8/R121 doi:10.1186/gb-2008-9-8-r121]


==Contents of Proteopedia==
==Contents of Proteopedia==
Currently, Proteopedia has {{NUMBEROFARTICLES}} [[Special:Allpages | articles]] (pages), and {{NUMBEROFUSERS}} [[Special:Listusers | registered users]].


Currently, Proteopedia has {{NUMBEROFARTICLES}} [[Special:Allpages | articles]] (pages), and {{NUMBEROFUSERS}} [[Special:Listusers | registered users]]. Among other pages, 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, 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.
==Most active contributors==
 
<table border='1'>
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 [[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]].
<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==
==Wishlist and Problems==
Please list desired new features on the page [[Proteopedia:Wishlist]] and problems you have encountered on the page [[Proteopedia: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==
==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.
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==
==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 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.-->


Proteopedia uses the [http://wiki.jmol.org/index.php/MediaWiki Jmol Extension to MediaWiki] created by Nicolas Vervelle and adapted by the Proteopedia team.
==Policy==
Please see [[Proteopedia:Policy]]


The [http://www.jmol.org Jmol java applet] is used to render the rotatable, zoomable macromolecular scenes.
==Credits==


The [http://kinemage.biochem.duke.edu/software/javamage.php MageJava] applet, by Jane and Dave Richardson is used to display kinemages.
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].


==Credits==
==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]


Proteopedia was created in 2007 at the Weizmann Institute of Science.  
==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] -->


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.
==Additional key references about Proteopedia==


[http://www.jmol.org Jmol] has been made what it is today by [http://jmol.sourceforge.net/history/ many dedicated volunteers] working for many years. Notable credit goes to
<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'/>
[http://www.stolaf.edu/people/hansonr/ Bob Hanson], Miguel Howard, and [http://www.cac.science.ru.nl/people/egonw/ Egon Willighagen].


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