Proteopedia:Overview: Difference between revisions
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'''Purpose:''' | |||
Proteopedia.Org<ref>PMID:21536137</ref><ref name="pubs">[[Proteopedia:About#How_to_cite_Proteopedia|Additional publications about Proteopedia.]]</ref> is a free, [https://en.wikipedia.org/wiki/Open_source open source], [https://en.wikipedia.org/wiki/Wiki wiki] encyclopedia of protein 3D molecular structure and function. | |||
Proteopedia. | |||
See [[Proteopedia:About#Proteopedia_Mission_Statement|Mission & Goals]]. | See [[Proteopedia:About#Proteopedia_Mission_Statement|Mission & Goals]]. | ||
'''History:''' | |||
Proteopedia was [[Proteopedia:About#Credits|created in 2007]] by [[Proteopedia:Team#Proteopedia_Founders_.26_Developers|three initial founders]] at the Weizmann Institute of Science, Rehovot, Israel. It was created after Wikipedia declined to include [[Jmol]] for molecular visualization. | Proteopedia was [[Proteopedia:About#Credits|created in 2007]] by [[Proteopedia:Team#Proteopedia_Founders_.26_Developers|three initial founders]] at the Weizmann Institute of Science, Rehovot, Israel. It was created after Wikipedia declined to include [[Jmol]] for molecular visualization. | ||
'''Unique & Powerful Capabilities:''' | |||
* [[JSmol]] displays interactive 3D protein molecules (see [[Proteopedia:About#Implementation|Implementation]]). | |||
* '''[[Phosphofructokinase (PFK)|{{Font color|#00b000|Green links}}]]''' change the 3D interactive molecular scene, showing what is described in the green-linked text. Example: [[Phosphofructokinase (PFK)]]. | |||
* [[Scene authoring tools|Molecular-scene authoring tools]] make it easy to customize molecular scenes. Proteopedia is the '''easiest place''' to create molecular scenes with the colors and renderings (solid, cartoon, ball and stick, etc.) you want. You use buttons and forms. No command language needed! [[Proteopedia:Video_Guide#Video_7:_Adding_scenes_.28green_links.29|Video Demonstration]]. Your scenes are '''immediately online'''. Use [http://firstglance.jmol.org FirstGlance in Jmol] to understand your macromolecule first. | |||
'''Contents:''' | |||
Proteopedia has two kinds of pages: | |||
* "Seeded" pages created automatically (no human involved) for each of the >200,000<ref name="now">In March, 2024.</ref> [[empirical models]] in the [[Protein Data Bank]]. Each seeded page is titled with a [[PDB code]]. Example: [[6zgg]]. | |||
* Human-authored pages. There are several thousand<ref name="now" /><ref name="mtds">The count depends on whether you exclude less-developed pages with almost no content. There are > 8,000 user-authored pages (excluding the namespaces for User pages, uploaded images, and Categories), but some have little content, and 3,200 of them, mostly student practice pages, contain the word [[Sandboxes|Sandbox]].</ref> user-authored pages. A well-developed example is [[Hemoglobin]]. Especially well-developed pages are assigned DOIs ([[Digital object identifier]]s), making them citable publications. [[Hemoglobin]] is an example, and see [[Special:PagesWithDOI|pages with DOIs]]. Some pages explain structural biology terminology and concepts (see [[About Macromolecular Structure]], >100<ref name="now" /> pages), while others analyse a single protein, or a family of proteins (see the [[Proteopedia:Structure_Index|Structure Index]], about 1,250<ref name="now" /> pages). | |||
'''Usage:''' | |||
Proteopedia pages have been viewed > [[Special:Statistics|300 million]] times since its inception. 109<ref name="now" /> user-authored pages have been viewed >50,000 times each (see [https://proteopedia.org/wiki/index.php?title=Special:Popularpages&limit=1000&offset=0 Popular pages]). [[Proteopedia:News#Adoptions_in_College_and_University_Classes|University Professors]] assign students to author content in Proteopedia. There are {{NUMBEROFUSERS}} user accounts, many for students, but only a fraction of the users have authored well-developed content. | |||
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'''Notes:''' | |||
<references /> | |||
Latest revision as of 06:55, 5 December 2024
Purpose: Proteopedia.Org[1][2] is a free, open source, wiki encyclopedia of protein 3D molecular structure and function. See Mission & Goals.
History: Proteopedia was created in 2007 by three initial founders at the Weizmann Institute of Science, Rehovot, Israel. It was created after Wikipedia declined to include Jmol for molecular visualization.
Unique & Powerful Capabilities:
- JSmol displays interactive 3D protein molecules (see Implementation).
- Green links change the 3D interactive molecular scene, showing what is described in the green-linked text. Example: Phosphofructokinase (PFK).
- Molecular-scene authoring tools make it easy to customize molecular scenes. Proteopedia is the easiest place to create molecular scenes with the colors and renderings (solid, cartoon, ball and stick, etc.) you want. You use buttons and forms. No command language needed! Video Demonstration. Your scenes are immediately online. Use FirstGlance in Jmol to understand your macromolecule first.
Contents: Proteopedia has two kinds of pages:
- "Seeded" pages created automatically (no human involved) for each of the >200,000[3] empirical models in the Protein Data Bank. Each seeded page is titled with a PDB code. Example: 6zgg.
- Human-authored pages. There are several thousand[3][4] user-authored pages. A well-developed example is Hemoglobin. Especially well-developed pages are assigned DOIs (Digital object identifiers), making them citable publications. Hemoglobin is an example, and see pages with DOIs. Some pages explain structural biology terminology and concepts (see About Macromolecular Structure, >100[3] pages), while others analyse a single protein, or a family of proteins (see the Structure Index, about 1,250[3] pages).
Usage: Proteopedia pages have been viewed > 300 million times since its inception. 109[3] user-authored pages have been viewed >50,000 times each (see Popular pages). University Professors assign students to author content in Proteopedia. There are 5,657 user accounts, many for students, but only a fraction of the users have authored well-developed content.
Notes:
- ↑ 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
- ↑ Additional publications about Proteopedia.
- ↑ 3.0 3.1 3.2 3.3 3.4 In March, 2024.
- ↑ The count depends on whether you exclude less-developed pages with almost no content. There are > 8,000 user-authored pages (excluding the namespaces for User pages, uploaded images, and Categories), but some have little content, and 3,200 of them, mostly student practice pages, contain the word Sandbox.