Proteopedia:About

From Proteopedia

Overview of Proteopedia

The Overview briefly introduces Purpose, History, Unique Capabilities, Types of Contents, and Usage Statistics. More details follow below.

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 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 Interactive 3D Complements - I3DCs.
• To develop new Teaching strategies using Proteopedia.

The Proteopedia Team

For a gallery of the Proteopedia Team, click here Additional photos of Proteopedia enthusiasts are in the Scrapbook.

Contents of Proteopedia

Currently, Proteopedia has 252,600 articles (pages), and 5,703 registered users.

Most active contributors

Seeded pages

Proteopedia contains one page for every entry in the 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 identification code, are "seeded" automatically to include a default view of the 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 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.

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 Mediawiki, which was adapted by the Proteopedia team for macromolecular scene authoring and other special features. Proteopedia uses the Jmol/JSmol Extension to MediaWiki created by Nicolas Vervelle and adapted by the Proteopedia team. The JSmol object is used to render the rotatable, zoomable macromolecular scenes.

Policy

Please see Proteopedia:Policy

Credits

Proteopedia was created in 2007 at the Weizmann Institute of Science by three initial founders and developers. Subsequent team members have helped make it what it is today. Proteopedia is supported by The Israel Structural Proteomics Center at the Weizmann Institute of Science, Rehovot, Israel. Jmol and JSmol have been made what they are today by many dedicated volunteers working for many years. Notable credit goes to Bob Hanson, Miguel Howard, and Egon Willighagen.

Support

• I-CORE: The Center of Research Excellence in Integrated Structural Cell Biology
• The Dana and Yossie Hollander Center for Structural Proteomics
• Weizmann Institute of Science
• ELIXIR

How to cite Proteopedia

• 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
• Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121

Additional key references about Proteopedia

• Prilusky, J. & Sussman, J.L. BLOG in eLife Sharing macromolecule concepts online with Proteopedia (2016).
• Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
• Prilusky J, Hodis E and Sussman JL. Proteopedia: Exciting Advances in the 3D Encyclopedia of Biomolecular Structure. Chapter Macromolecular Crystallography, Part of the series NATO Science for Peace and Security Series A: Chemistry and Biology pp 149-161, 2011 doi:http://dx.doi.org/10.1007/978-94-007-2530-0_14
• 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
• Hodis E, Prilusky J, Sussman JL. Proteopedia: A collaborative, virtual 3D web-resource for protein and biomolecule structure and function. Biochem Mol Biol Educ. 2010 Sep;38(5):341-2. doi: 10.1002/bmb.20431. PMID:21567857 doi:10.1002/bmb.20431
• Hodis E, Prilusky J, Sussman JL. Proteopedia: A collaborative, virtual 3D web-resource for protein and biomolecule structure and function. Biochem Mol Biol Educ. 2010 Sep;38(5):341-2. doi: 10.1002/bmb.20431. PMID:21567857 doi:10.1002/bmb.20431
• Hodis, E., Prilusky, J., & Sussman, J.L. in From Molecules to Medicines (2009). Tools to Make 3D Structural Data More Comprehensible: Emovie & Proteopedia pg. 169-182.
• Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL. Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules. Genome Biol. 2008;9(8):R121. Epub 2008 Aug 3. PMID:18673581 doi:http://dx.doi.org/10.1186/gb-2008-9-8-r121

Contact

If you have any questions, please 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.