Profile-based short linear protein motif discovery [PDF]
BMC Bioinformatics, 2012 Background Short linear protein motifs are attracting increasing attention as functionally independent sites, typically 3–10 amino acids in length that are enriched in disordered regions of proteins.
Haslam Niall J, Shields Denis C
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iELM--a web server to explore short linear motif-mediated interactions. [PDF]
Nucleic Acids Research, 2012 The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive.
Holger Dinkel +2 more
exaly +11 more sources
A correlated motif approach for finding short linear motifs from protein interaction networks [PDF]
BMC Bioinformatics, 2006 Background An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expensive.
Hugo Willy +3 more
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Computational identification and analysis of protein short linear motifs [PDF]
Frontiers in Bioscience, 2010 Short linear motifs (SLiMs) in proteins can act as targets for proteolytic cleavage, sites of post-translational modification, determinants of sub-cellular localization, and mediators of protein-protein interactions.
Davey, Norman E. +2 more
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The SLiMDisc server: short, linear motif discovery in proteins [PDF]
Nucleic Acids Research, 2007 Short, linear motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. Overrepresentation of convergent occurrences of motifs in proteins with a common attribute (such as similar subcellular location
Davey, Norman E. +5 more
core +6 more sources
QSLiMFinder: improved short linear motif prediction using specific query protein data. [PDF]
Bioinformatics, 2015 MOTIVATION: The sensitivity of de novo short linear motif (SLiM) prediction is limited by the number of patterns (the motif space) being assessed for enrichment.
Nicolas Palopoli, Richard J. Edwards
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Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling. [PDF]
Molecular Cell, 2020 Short linear motifs (SLiMs) drive dynamic protein-protein interactions essential for signaling, but sequence degeneracy and low binding affinities make them difficult to identify.
Yadav, V.
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Thousands of protein linear motif classes may still be undiscovered. [PDF]
PLoS ONE, 2021 Linear motifs are short protein subsequences that mediate protein interactions. Hundreds of motif classes including thousands of motif instances are known. Our theory estimates how many motif classes remain undiscovered.
Denys Bulavka +4 more
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Evidence for the concerted evolution between short linear protein motifs and their flanking regions. [PDF]
PLoS ONE, 2009 BACKGROUND: Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur
Claudia Chica +2 more
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Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins [PDF]
BMC Bioinformatics, 2010 Background Large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins. However, existing methods for estimating the probability of motif recurrence may be biased by the
Davey Norman E +2 more
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