Short linear motifs in intrinsically disordered regions modulate HOG signaling capacity. [PDF]
BMC Syst Biol, 2018 AbstractThe 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).
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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. Computational discovery of SLiMs involves assembling a group of proteins postulated to share a potential motif, masking out residues less
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 or a shared interaction partner) provides a feasible means to discover novel occurrences ...
Davey, Norman E. +2 more
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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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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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The Parallelism Motifs of Genomic Data Analysis [PDF]
, 2020 Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data ...
Awan, Muaaz +13 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
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SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent [PDF]
Nucleic Acids Research, 2006 Many important interactions of proteins are facilitated by short, linear motifs (SLiMs) within a protein's primary sequence. Our aim was to establish robust methods for discovering putative functional motifs. The strongest evidence for such motifs is obtained when the same motifs occur in unrelated proteins, evolving by convergence.
Davey, Norman E. +2 more
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SLiMScape: a protein short linear motif analysis plugin for Cytoscape [PDF]
BMC Bioinformatics, 2013 Abstract Background Computational protein short linear motif discovery can use protein interaction information to search for motifs among proteins which share a common interactor. Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly visualize motifs in a network of ...
O’Brien, Kevin T +2 more
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Structural Mechanism for the Specific Assembly and Activation of the Extracellular Signal Regulated Kinase 5 (ERK5) Module [PDF]
, 2013 Mitogen-activated protein kinase (MAPK) activation depends on a linear binding motif found in all MAPK kinases (MKK). In addition, the PB1 (Phox and Bem1) domain of MKK5 is required for extracellular signal regulated kinase 5 (ERK5) activation.
Aberg +57 more
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