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Exploring Short Linear Motifs Using the ELM Database and Tools
Current Protocols in Bioinformatics, 2017 The Eukaryotic Linear Motif (ELM) resource is dedicated to the characterization and prediction of short linear motifs (SLiMs). SLiMs are compact, degenerate peptide segments found in many proteins and essential to almost all cellular processes.
Marc Gouw, Holger Dinkel, Toby J. Gibson
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Mimicry of Short Linear Motifs by Bacterial Pathogens: A Drugging Opportunity
Trends in Biochemical Sciences, 2020Bacterial pathogens have developed complex strategies to successfully survive and proliferate within their hosts. Throughout the infection cycle, direct interaction with host cells occurs. Many bacteria have been found to secrete proteins, such as effectors and toxins, directly into the host cell with the potential to interfere with cell regulatory ...
Toby J. Gibson, Hugo Sámano-Sánchez
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Stressing the role of a short linear motif in ataxin-2 condensation
Molecular Cell, 2023Ataxin-2, an RNA-binding protein that is conserved across eukaryotes, is involved in stress granule assembly and age-associated neurodegenerative diseases. In this issue of Molecular Cell, Boeynaems et al.1 identify a short linear motif in ataxin-2 as a condensation switch, providing molecular insights into its essential role in cellular stress ...
Scheidt, Tom +3 more
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How to Annotate and Submit a Short Linear Motif to the Eukaryotic Linear Motif Resource
2020Over the past few years, it has become apparent that approximately 35% of the human proteome consists of intrinsically disordered regions. Many of these disordered regions are rich in short linear motifs (SLiMs) which mediate protein-protein interactions. Although these motifs are short and often partially conserved, they are involved in many important
Gouw, Marc +8 more
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SLiMSearch: A Webserver for Finding Novel Occurrences of Short Linear Motifs in Proteins, Incorporating Sequence Context [PDF]
Lecture Notes in Computer Science, 2010 Short, linear motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch (Short, Linear Motif Search) webserver is a flexible tool that enables researchers to identify novel occurrences of predefined SLiMs in sets of proteins ...
Richard J. Edwards +2 more
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Degrons and degradation signals beyond short linear motifs
Nature Chemical BiologyUbiquitin-dependent protein degradation regulates myriad fundamental cellular processes. At its core are degradation signals, or degrons, that initiate substrate engagement and ubiquitination by E3 ubiquitin ligases. Here we highlight how a variety of degradation signals promote substrate-E3 ligase interactions to orchestrate protein turnover with ...
Baiyun Wang, Ning Zheng
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Screening Intrinsically Disordered Regions for Short Linear Binding Motifs
2020The intrinsically disordered regions of the proteome are enriched in short linear motifs (SLiMs) that serve as binding sites for peptide binding proteins. These interactions are often of low-to-mid micromolar affinities and are challenging to screen for experimentally.
Muhammad, Ali +2 more
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How viral proteins bind short linear motifs and intrinsically disordered domains
Essays in Biochemistry, 2022Abstract Viruses are the obligate intracellular parasites that exploit the host cellular machinery to replicate their genome. During the viral life cycle viruses manipulate the host cell through interactions with host proteins. Many of these protein–protein interactions are mediated through the recognition of host globular domains by ...
Priyanka Madhu +2 more
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Identifying Protein Short Linear Motifs by Position-Specific Scoring Matrix
2016Short linear motifs (SLiMs) play a central role in several biological functions, such as cell regulation, scaffolding, cell signaling, post-translational modification, and cleavage. Identifying SLiMs is an important step for understanding their functions and mechanism.
Chun Fang +3 more
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Prediction of Biological Protein-protein Interaction Types Using Short-Linear Motifs
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, 2013Protein-protein interactions (PPIs) play a key role in many biological processes and functions in living cells. Thus, identification, prediction, and analysis of PPIs are important aspects in molecular biology. We propose a computational model to predict biological PPI types using short-linear motifs (SLiMs).
Manish Pandit +2 more
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