3-D Protein Encyclopedia is Interactive
A free collaborative Web site is providing a new resource for biologists and biochemists by linking written information and 3-D structural
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information. Proteopedia, a wiki Web resource, displays protein, RNA, DNA and other macromolecules, as well as their assemblies and interactions with small molecules, in an interactive format. Images are surrounded by descriptive text containing hyperlinks that change the appearance (such as view, representations, colors or labels) of the adjacent 3-D structure to reflect the concept explained in the text.
Designed 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, Proteopedia is fully and freely accessible to the public, and its pages can be created and edited by registered users. Aside from content added by Proteopedia’s existing users, pages on each of the more than 50,000 entries in the World Wide Protein Data Bank have been automatically created, providing pages that are already useful and primed for expansion by users.
Currently, the Proteopedia site reports that it has 53,822 articles (pages), and 157 registered users. The site 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.
Proteopedia was developed at the Weizmann Institute of Science in Israel by Jaime Prilusky, Eran Hodis, and Joel L. Sussman, together with colleagues at the Weizmann Institute and in the USA. It was built with Mediawiki, which was adapted by the Proteopedia team for macromolecular scene authoring and other special features. It uses the Jmol Extension to MediaWiki created by Nicolas Vervelle and adapted by the Proteopedia team. The Jmol java applet is used to render the rotatable, zoomable macromolecular scenes; the MageJava applet, by Jane and Dave Richardson is used to display kinemages.
Related Resources
1. www.proteopedia.org
2. Proteopedia Video Guide: www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide
3. Proteopedia, Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL, Genome Biology (3 August 2008), genomebiology.com/2008/9/8/R121
