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Nucleic Acids Research 2005 33(Web Server Issue):W249-W251; doi:10.1093/nar/gki363
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Fragnostic: walking through protein structure space

Iddo Friedberg* and Adam Godzik

The Burnham Institute 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA

*To whom correspondence should be addressed. Tel: +1 858 646 3100; Fax: +1 858 713 9925; Email: idoerg{at}burnham.org

Received February 8, 2005. Revised February 23, 2005. Accepted February 23, 2005.

The Fragnostic (http://ffas.burnham.org/Fragnostic) web tool implements a novel and useful view of protein structure space. We mined a non-redundant subset of the PDB for common fragments shared between proteins inhabiting different SCOP folds. Subsequently, we formulated an inter-fold similarity measure based on fragment sharing. Fold space is described as a graph whose nodes are folds between which the edges are drawn depending on the extent of fragment sharing. In this fashion, Fragnostic helps discover meaningful relationships between proteins belonging to different folds, based on sharing similar fragments in the proteins comprising those folds. Distant fold similarity information is supplemented by annotations taken from Gene Ontology, SCOP and CATH. Overall, Fragnostic is a tool which helps discover structural and functional relationships between proteins which are distantly related or seemingly unrelated.


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I. Friedberg
Automated protein function prediction--the genomic challenge
Brief Bioinform, September 1, 2006; 7(3): 225 - 242.
[Abstract] [Full Text] [PDF]


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