Exploring Short Linear Motifs Using the ELM Database and Tools

Gouw, Marc; Sámano-Sánchez, Hugo; Roey, Kim Van; Diella, Francesca; Gibson, Toby J.; Dinkel, Holger

doi:10.1002/cpbi.26

Cited by 32 publications

(23 citation statements)

References 51 publications

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“…Nevertheless, the graphical user interface is not suitable for automated or large scale analyses. One of the latest updates to the ELM resource has been to include an application programmatic interface (API) to the ELM exploration pipeline ( 30 ). The ELM exploration API allows users to submit either a protein sequence or a UniProt ID to predict which SLiMs might exist in it.…”

Section: New Features In Elmmentioning

confidence: 99%

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The eukaryotic linear motif resource – 2018 update

Gouw

Michael

Sámano-Sánchez

et al. 2017

Nucleic Acids Research

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192

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Short linear motifs (SLiMs) are protein binding modules that play major roles in almost all cellular processes. SLiMs are short, often highly degenerate, difficult to characterize and hard to detect. The eukaryotic linear motif (ELM) resource (elm.eu.org) is dedicated to SLiMs, consisting of a manually curated database of over 275 motif classes and over 3000 motif instances, and a pipeline to discover candidate SLiMs in protein sequences. For 15 years, ELM has been one of the major resources for motif research. In this database update, we present the latest additions to the database including 32 new motif classes, and new features including Uniprot and Reactome integration. Finally, to help provide cellular context, we present some biological insights about SLiMs in the cell cycle, as targets for bacterial pathogenicity and their functionality in the human kinome.

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Section: New Features In Elmmentioning

confidence: 99%

“…The API can be accessed using any programming framework that can process HTTP requests, for example wget, curl and the python ‘requests’ package. For more information on using the API, usage guidelines and how to interpret the results, see ( 30 ) and read the documentation on elm.eu.org/api/manual.html .…”

Section: New Features In Elmmentioning

confidence: 99%

The eukaryotic linear motif resource – 2018 update

Gouw

Michael

Sámano-Sánchez

et al. 2017

Nucleic Acids Research

Self Cite

192

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“…ELM has also spun-off several specialized databases: phospho.ELM for phosphorylation sites with experimental evidence [71], switches.ELM for conditional molecular switches, such as requiring that a site be modified [72], and iELM, with an emphasis on protein-protein interactions [73]. A detailed tutorial provides orientation for ELM use [74].…”

Section: Motif Databasesmentioning

confidence: 99%

Resources to Discover and Use Short Linear Motifs in Viral Proteins

Hraber

O’Maille

Silberfarb

et al. 2020

Trends in Biotechnology

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Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.

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“…Signal peptides were predicted using SignalP [42]. Linear motifs participating in binding events were retrieved from the ELM database [43], considering only "LIG/DOC" classes. The ELM prediction was also utilized, considering only those hits that passed the various filters as described by Gouw et al [43].…”

Section: Annotation and Prediction Of Protein Propertiesmentioning

confidence: 99%

Occurrence of ordered and disordered structural elements in postsynaptic proteins supports optimization for interaction diversity

Kiss-Toth

Dobson

Péterfia

et al. 2018

Preprint

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The human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, contributing to a high level of protein modularity. We introduce structure and regulation based descriptors to assess the diversity of interactions required to maintain the synaptic plasticity. Our approach reveals that the postsynaptic proteome has markedly different features compared to those of other proteins included in the human proteome. Graphical abstractKey terms

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Exploring Short Linear Motifs Using the ELM Database and Tools

Cited by 32 publications

References 51 publications

The eukaryotic linear motif resource – 2018 update

The eukaryotic linear motif resource – 2018 update

Resources to Discover and Use Short Linear Motifs in Viral Proteins

Occurrence of ordered and disordered structural elements in postsynaptic proteins supports optimization for interaction diversity

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