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Nucleic Acids Res. 2011 Jul;39(Web Server issue):W203-9. doi: 10.1093/nar/gkr410. Epub 2011 Jun 10.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

Author information

1
INSERM, U973, Université Paris 7-Paris Diderot, UMR-S973, MTi F-75013 Paris, France. leslie.regad@univ-paris-diderot.fr

Abstract

The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

PMID:
21665924
PMCID:
PMC3125790
DOI:
10.1093/nar/gkr410
[Indexed for MEDLINE]
Free PMC Article

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