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

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


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

MeSH terms

  • Amino Acid Motifs*
  • Internet
  • Protein Folding
  • Sequence Analysis, Protein
  • Software*