A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences [PDF]
BMC Bioinformatics, 2008 Background The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs.
López Rodrigo +4 more
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Orchestrating serine/threonine phosphorylation and elucidating downstream effects by short linear motifs. [PDF]
Biochem J, 2022 Cellular function is based on protein–protein interactions. A large proportion of these interactions involves the binding of short linear motifs (SLiMs) by folded globular domains. These interactions are regulated by post-translational modifications, such as phosphorylation, that create and break motif binding sites or tune the affinity of the ...
Kliche J, Ivarsson Y.
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Redefining the BH3 Death Domain as a ‘Short Linear Motif’ [PDF]
Trends in Biochemical Sciences, 2015 B cell lymphoma-2 (BCL-2)-related proteins control programmed cell death through a complex network of protein-protein interactions mediated by BCL-2 homology 3 (BH3) domains. Given their roles as dynamic linchpins, the discovery of novel BH3-containing proteins has attracted considerable attention.
Aouacheria, Abdel +3 more
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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. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional
Robert J. Weatheritt +3 more
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Systematic discovery of new recognition peptides mediating protein interaction networks. [PDF]
PLoS Biology, 2005 Many aspects of cell signalling, trafficking, and targeting are governed by interactions between globular protein domains and short peptide segments. These domains often bind multiple peptides that share a common sequence pattern, or "linear motif" (e.g.,
Victor Neduva +9 more
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HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons. [PDF]
Nucleic Acids Res, 2017 Short linear motifs (SLiMs) in proteins are self-sufficient functional sequences that specify interaction sites for other molecules and thus mediate a multitude of functions. Computational, as well as experimental biological research would significantly benefit, if SLiMs in proteins could be correctly predicted de novo with high sensitivity.
Prytuliak R +3 more
europepmc +11 more sources
Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins. [PDF]
, 2010 Background: large datasets of protein interactions provide a rich resource for the discovery of Short Linear Motifs (SLiMs) that recur in unrelated proteins.
Davey, Norman E. +8 more
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Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. [PDF]
PLoS Computational Biology, 2014 Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization.
Alex N Nguyen Ba +7 more
doaj +1 more source
Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. [PDF]
BMC Syst Biol, 2018 Abstract The effort to characterize intrinsically disordered regions of signaling proteins is rapidly expanding. An important class of disordered interaction modules are ubiquitous and functionally diverse elements known as short linear motifs (SLiMs).
Strome B +5 more
europepmc +6 more sources
Evolution of Directed Triangle Motifs in the Google+ OSN [PDF]
, 2015 Motifs are a fundamental building block and distinguishing feature of networks. While characteristic motif distribution have been found in many networks, very little is known today about the evolution of network motifs.
Uhlig, S +4 more
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