Proteopedia- a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules

Table 1 Unique features of Proteopedia in comparison to existing resources with similar purposes

Resource	Purpose	Contents (April 2008)	Web resource	Contains all entries in the PDB, updated automatically	Community annotation	Interactive three-dimensional within site with molecular scenes linked to text	User-friendly three-dimensional authoring tools, freely available
Proteopedia	A free, collaborative, three-dimensional encyclopedia of proteins and other molecules	One page for every PDB entry with abstract and interactive three-dimensional views, including functional sites and ligands (> 50,000 pages), plus several dozen well-developed higher-level pages (such as hemoglobin)	Yes	Yes	Yes	Yes	Yes
iSee	To communicate the results of the SGC and ideally of other groups that purchase the software	Results of the Structural Genomics Consortium (about 400 datapacks available)	No*	No	No^†	Yes	No^‡
Kinemage	To communicate scientific illustrations as interactive computer displays	Estimated to be in the thousands for a wide variety of proteins and biomacromolecules, and created by a diverse group of authors	No*	No	No^†	Yes	Yes
TOPSAN	An annotation platform limited to the targets of the Protein Structure Initiative	Small subset of structural genomics results (< 2,000 pages)	Yes	No	Yes ^§	No	No
PDBWiki	A community annotated knowledge base of biological molecular structures	One-to-one mapping of the PDB with additional links and images (> 50,000 pages)	Yes	Yes	Yes	No	No

This table is limited to publicly accessible web resources for information on protein and macromolecules that emphasize macromolecular three-dimensional structure and permit community annotation. The requirement for permitting community annotation excludes resources such as OCA, PDB, JenaLib, and PDBSum. The requirement to emphasize macromolecular three-dimensional structure excludes resources such as Wikipedia. (see the resource websites [39, 47–50]). *The option to display datapacks (called kinemages in the case of Kinemage) on the web exists, but no web resource exists with pages displaying each of the datapacks. ^†Using the authoring tools, users may create new datapacks. In this sense, the datapacks available on the web are community annotated. However, datapacks do not evolve via expert community annotation like a wiki. ^‡The authoring tools are commercially available. ^§Most of the content of TOPSAN pages is fixed, but users can add/edit a Protein Summary section and add comments.

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