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SA-Mot: a web server for the identification of motifs of interest extracted from protein loops
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 focu...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125790/ https://www.ncbi.nlm.nih.gov/pubmed/21665924 http://dx.doi.org/10.1093/nar/gkr410 |
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author | Regad, Leslie Saladin, Adrien Maupetit, Julien Geneix, Colette Camproux, Anne-Claude |
author_facet | Regad, Leslie Saladin, Adrien Maupetit, Julien Geneix, Colette Camproux, Anne-Claude |
author_sort | Regad, Leslie |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3125790 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-31257902011-07-05 SA-Mot: a web server for the identification of motifs of interest extracted from protein loops Regad, Leslie Saladin, Adrien Maupetit, Julien Geneix, Colette Camproux, Anne-Claude Nucleic Acids Res Articles 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. Oxford University Press 2011-07-01 2011-06-10 /pmc/articles/PMC3125790/ /pubmed/21665924 http://dx.doi.org/10.1093/nar/gkr410 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Regad, Leslie Saladin, Adrien Maupetit, Julien Geneix, Colette Camproux, Anne-Claude SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title | SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title_full | SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title_fullStr | SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title_full_unstemmed | SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title_short | SA-Mot: a web server for the identification of motifs of interest extracted from protein loops |
title_sort | sa-mot: a web server for the identification of motifs of interest extracted from protein loops |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125790/ https://www.ncbi.nlm.nih.gov/pubmed/21665924 http://dx.doi.org/10.1093/nar/gkr410 |
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