ReviewCell communication and signaling : CCS2015
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.
Review in Cell communication and signaling : CCS, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.Nature communications · 2026Article
- A quantitative intracellular peptide binding assay reveals recognition determinants and context dependence of short linear motifs.bioRxiv : the preprint server for biology · 2024Article
- From interaction networks to interfaces, scanning intrinsically disordered regions using AlphaFold2.Nature communications · 2024Article
- Discovery and Characterization of Linear Motif Mediated Protein-Protein Complexes.Advances in experimental medicine and biology · 2024Article
- Exploiting the endogenous yeast nuclear proteome to identify short linear motifs in vivo.Cell reports methods · 2023Article
- A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation.Nucleic acids research · 2023Article
- A Structural Network Analysis of Neuronal ArhGAP21/23 Interactors by Computational Modeling.ACS omega · 2023Article
- The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs.RSC advances · 2023Review
- How different viruses perturb host cellular machinery via short linear motifs.EXCLI journal · 2023Review
- The interaction between LC8 and LCA5 reveals a novel oligomerization function of LC8 in the ciliary-centrosome system.Scientific reports · 2022Article
- Comparative Analysis of Structural Features in SLiMs from Eukaryotes, Bacteria, and Viruses with Importance for Host-Pathogen Interactions.Pathogens (Basel, Switzerland) · 2022Article
- Degron masking outlines degronons, co-degrading functional modules in the proteome.Communications biology · 2022Article
- Function of SYDE C2-RhoGAP family as signaling hubs for neuronal development deduced by computational analysis.Scientific reports · 2022Article
- Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates.Scientific reports · 2022Article
- The Eukaryotic Linear Motif resource: 2022 release.Nucleic acids research · 2022Article
- Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit theFrontiers in microbiology · 2022Article
- Short linear motif candidates in the cell entry system used by SARS-CoV-2 and their potential therapeutic implications.Science signaling · 2021Review
- Article
- Computational Biology and Machine Learning Approaches to Understand Mechanistic Microbiome-Host Interactions.Frontiers in microbiology · 2021Review
- Large-scale survey and database of high affinity ligands for peptide recognition modules.Molecular systems biology · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has become clear in outline though not yet in detail how cellular regulatory and signalling systems are constructed. The essential machines are protein complexes that effect regulatory decisions by undergoing internal changes of state. Subcomponents of these cellular complexes are assembled into molecular switches. Many of these switches employ one or more short peptide motifs as toggles that can move between one or more sites within the switch system, the simplest being on-off switches. Paradoxically, these motif modules (termed short linear motifs or SLiMs) are both hugely abundant but difficult to research. So despite the many successes in identifying short regulatory protein motifs, it is thought that only the "tip of the iceberg" has been exposed. Experimental and bioinformatic motif discovery remain challenging and error prone. The advice presented in this article is aimed at helping researchers to uncover genuine protein motifs, whilst avoiding the pitfalls that lead to reports of false discovery.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.