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Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W249-51.

Fragnostic: walking through protein structure space.

Author information

1
The Burnham Institute 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. idoerg@burnham.org

Abstract

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.

PMID:
15980462
PMCID:
PMC1160124
DOI:
10.1093/nar/gki363
[Indexed for MEDLINE]
Free PMC Article

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