Friday, January 30, 2009

Protein Wikis

Genome Biology has published an article: "Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules"

New Media is making inroads to scientific publishing. The traditional model of scientific publishing is peer-review then publish, but the Wiki model is publish then peer-review. While it's not to the point that a Wiki-edit would show up on someone's publication list, Wiki style articles for high-throughput genomics/proteomics experiments make sense.
A protein structure used to be enough work and new research material to support an entire PhD dissertation, but now with high throughput protein structure determination pipelines like PSI, a more informal publishing structure is needed. Wiki's offer the ability for scientific notes to published for each of the catalogued protein structures, without having to do a publication for each and every one of the +50K protein structures stored in the Protein Data Bank.

There are a few different Protein Structure Wiki's that are getting started:

  • Proteopedia : Seeks to annotate known protein structures with Biologically relevant information.

  • Topsan : Sub-project of the Protein Structure Initiative and The Joint Center of Structural Genomics. Used to annotate proteins generated in high throughput Protein structure determination pipeline. Many of the targets were originally selected in batches and have no known biological information.

  • PDBWiki : Seems more geared toward discussion of the of the characteristics of the models themselves (ie density maps and collision errors)

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