Proteopedia:Overview
From Proteopedia
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 nearly 250,000[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[4][5] user-authored pages. Authorship is collaborative: content can be expanded or updated long after the page was created, with different users contributing. 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[4] pages), while others analyse a single protein, or a family of proteins (see the Structure Index, about 1,250[4] pages).
Usage: Proteopedia pages have been viewed nearly half a billion times since its inception. 109[4] user-authored pages have been viewed >50,000 times each (see Popular pages). University Professors assign students to author content in Proteopedia. There are 5,993 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.
- ↑ In January, 2026.
- ↑ 4.0 4.1 4.2 4.3 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.
