Life Isn't 2-D, So Why Should Our Encyclopedias Be?

Main Category: Biology / Biochemistry
Also Included In: IT / Internet / E-mail
Article Date: 25 Aug 2008 - 1:00 PDT

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Biologists and biochemists are now able to access 3D images of biomacromolecules underlying biological functions and disease. Rather than relying on text to provide the understanding of biomacromolecule structures, a collaborative website called Proteopedia now provides a new resource by linking written information and three-dimensional structural information. The wiki web resource, first described in BioMed Central's open access journal Genome Biology, displays protein structures and other biomacromolecules in interactive format. These interactive images are surrounded by descriptive text containing hyperlinks that change the appearance (such as view, representations, colors or labels) of the adjacent 3D structure to reflect the concept explained in the text. This makes the complex structural information readily accessible and comprehensible, even to people who are not structural biologists.

The resource 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. According to Sussman, "Using Proteopedia, anyone can easily create descriptions of biomacromolecules linked to their 3D structure."

Aside from content added by Proteopedia's existing users, pages on each of the more than 50,000 entries in the Protein Data Bank have been automatically created with 'seed' information, creating pages that are already useful and primed for expansion by users. Members of the scientific community are invited to request a user account to edit existing pages and to create new ones.

Hodis says, "We are presenting Proteopedia to the scientific community to judge its usefulness and merit, and we truly hope that it will offer an effective and appealing way to convey the link between 3D structure and function."

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Article adapted by Medical News Today from original press release.
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1. Proteopedia
Hodis E, Prilusky J, Martz E, Silman I, Moult J, Sussman JL
Genome Biology (3 August 2008)
http://genomebiology.com/2008/9/8/R121
Article available at the journal website: http://genomebiology.com/

2. For a demonstration of the Proteopedia software, please visit the 'Proteopedia Video Guide' [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] where you will find several narrated videos to guide you through using Proteopedia.

3. Proteopedia (http://www.proteopedia.org/) is fully and freely accessible to the public, and Proteopedia pages can be created and edited by registered users. There is an accompanying narrated video guide to the website.

To provide additional incentive for giving editing pages a try, Proteopedia is holding a "Page of the Year" competition with an Apple iPod Touch (32GB) as the grand prize, donated by Apple's representative in Israel, iDigital.

4. Prilusky is Head of the Bioinformatics Unit at the Israel Structural Proteomics Center (http://www.weizmann.ac.il/ISPC). Hodis is a graduate student at the Feinberg Graduate School of the Weizmann Institute of Science. Sussman is former Head of the Protein Data Bank.

5. Genome Biology (http://genomebiology.com/) publishes articles from the full spectrum of biology. Subjects covered include any aspect of molecular, cellular, organismal or population biology studied from a genomic perspective, as well as genomics, proteomics, bioinformatics, genomic methods (including structure prediction), computational biology, sequence analysis (including large-scale and cross-genome analyses), comparative biology and evolution. Genome Biology has an impact factor of 7.12.

6. BioMed Central (http://www.biomedcentral.com/) is an independent online publishing house committed to providing immediate access without charge to the peer-reviewed biological and medical research it publishes. This commitment is based on the view that open access to research is essential to the rapid and efficient communication of science.

Source: Charlotte Webber
BioMed Central