Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.

Handle URI:
http://hdl.handle.net/10754/596841
Title:
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.
Authors:
Sayadi, Ahmed; Briganti, Leonardo; Tramontano, Anna; Via, Allegra
Abstract:
The function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length of the motifs and their variable degree of conservation makes their identification hard since it is difficult to correctly estimate the statistical significance of their occurrence. Consequently, only a small fraction of them have been discovered so far. We describe here an approach for the discovery of SLiMs based on their occurrence in evolutionarily unrelated proteins belonging to the same biological, signalling or metabolic pathway and give specific examples of its effectiveness in both rediscovering known motifs and in discovering novel ones. An automatic implementation of the procedure, available for download, allows significant motifs to be identified, automatically annotated with functional, evolutionary and structural information and organized in a database that can be inspected and queried. An instance of the database populated with pre-computed data on seven organisms is accessible through a publicly available server and we believe it constitutes by itself a useful resource for the life sciences (http://www.biocomputing.it/modipath).
Citation:
Sayadi A, Briganti L, Tramontano A, Via A (2011) Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs. PLoS ONE 6: e22270. Available: http://dx.doi.org/10.1371/journal.pone.0022270.
Publisher:
Public Library of Science (PLoS)
Journal:
PLoS ONE
KAUST Grant Number:
KUK-I1-012-43
Issue Date:
20-Jul-2011
DOI:
10.1371/journal.pone.0022270
PubMed ID:
21799808
PubMed Central ID:
PMC3140502
Type:
Article
ISSN:
1932-6203
Sponsors:
This work was partially supported by Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST: http://www.kaust.edu.sa/), by Fondazione Roma (http://www.fondazioneroma.it/it/index.html) and by the Italian Ministry of Health (http://www.salute.gov.it/), contract no. onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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Publications Acknowledging KAUST Support

Full metadata record

DC FieldValue Language
dc.contributor.authorSayadi, Ahmeden
dc.contributor.authorBriganti, Leonardoen
dc.contributor.authorTramontano, Annaen
dc.contributor.authorVia, Allegraen
dc.date.accessioned2016-02-21T09:35:10Zen
dc.date.available2016-02-21T09:35:10Zen
dc.date.issued2011-07-20en
dc.identifier.citationSayadi A, Briganti L, Tramontano A, Via A (2011) Exploiting Publicly Available Biological and Biochemical Information for the Discovery of Novel Short Linear Motifs. PLoS ONE 6: e22270. Available: http://dx.doi.org/10.1371/journal.pone.0022270.en
dc.identifier.issn1932-6203en
dc.identifier.pmid21799808en
dc.identifier.doi10.1371/journal.pone.0022270en
dc.identifier.urihttp://hdl.handle.net/10754/596841en
dc.description.abstractThe function of proteins is often mediated by short linear segments of their amino acid sequence, called Short Linear Motifs or SLiMs, the identification of which can provide important information about a protein function. However, the short length of the motifs and their variable degree of conservation makes their identification hard since it is difficult to correctly estimate the statistical significance of their occurrence. Consequently, only a small fraction of them have been discovered so far. We describe here an approach for the discovery of SLiMs based on their occurrence in evolutionarily unrelated proteins belonging to the same biological, signalling or metabolic pathway and give specific examples of its effectiveness in both rediscovering known motifs and in discovering novel ones. An automatic implementation of the procedure, available for download, allows significant motifs to be identified, automatically annotated with functional, evolutionary and structural information and organized in a database that can be inspected and queried. An instance of the database populated with pre-computed data on seven organisms is accessible through a publicly available server and we believe it constitutes by itself a useful resource for the life sciences (http://www.biocomputing.it/modipath).en
dc.description.sponsorshipThis work was partially supported by Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST: http://www.kaust.edu.sa/), by Fondazione Roma (http://www.fondazioneroma.it/it/index.html) and by the Italian Ministry of Health (http://www.salute.gov.it/), contract no. onc_ord 25/07, FIRB ITALBIONET and PROTEOMICA. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.en
dc.publisherPublic Library of Science (PLoS)en
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.en
dc.subject.meshDatabases, Proteinen
dc.titleExploiting publicly available biological and biochemical information for the discovery of novel short linear motifs.en
dc.typeArticleen
dc.identifier.journalPLoS ONEen
dc.identifier.pmcidPMC3140502en
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma Tor Vergata, Rome, Italyen
dc.contributor.institutionUniversita degli Studi di Roma La Sapienza, Rome, Italyen
kaust.grant.numberKUK-I1-012-43en

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