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HH-MOTiF: de novo detection of short linear motifs in proteins by Hidden Markov Model comparisons. [PDF]
Nucleic Acids Research, 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.
Bianca Habermann
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Exploring Short Linear Motifs Using the ELM Database and Tools
Current Protocols in Bioinformatics, 2017AbstractThe 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. However, despite their abundance, SLiMs remain largely uncharacterized.
Gouw, M. +5 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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ELM 2016--data update and new functionality of the eukaryotic linear motif resource.
Nucleic Acids Research, 2016 The Eukaryotic Linear Motif (ELM) resource (http://elm.eu.org) is a manually curated database of short linear motifs (SLiMs). In this update, we present the latest additions to this resource, along with more improvements to the web interface.
Norman Davey, Manjeet Kumar, Bora Uyar
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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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Use of viral motif mimicry improves the proteome-wide discovery of human linear motifs
Cell Reports, 2022Bishoy Wadie +2 more
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Proceedings of the National Academy of Sciences of the United States of America, 2022
Didier Vertommen +2 more
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Didier Vertommen +2 more
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