Exploring Short Linear Motifs Using the ELM Database and Tools

Marc Gouw1, Hugo Sámano‐Sánchez1, Kim Van Roey1, Francesca Diella1, Toby J. Gibson1, Holger Dinkel2

1 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 2 Leibniz‐Institute on Aging—Fritz Lipmann Institute (FLI), Jena
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 8.22
DOI:  10.1002/cpbi.26
Online Posting Date:  June, 2017
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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. However, despite their abundance, SLiMs remain largely uncharacterized. The ELM database is a collection of manually annotated SLiM instances curated from experimental literature. In this article we illustrate how to browse and search the database for curated SLiM data, and cover the different types of data integrated in the resource. We also cover how to use this resource in order to predict SLiMs in known as well as novel proteins, and how to interpret the results generated by the ELM prediction pipeline. The ELM database is a very rich resource, and in the following protocols we give helpful examples to demonstrate how this knowledge can be used to improve your own research. © 2017 by John Wiley & Sons, Inc.

Keywords: short linear motifs; bioinformatics; protein‐protein interaction; molecular switches; cell regulation

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Table of Contents

  • Introduction
  • Basic Protocol 1: Exploring the Content of the ELM Database
  • Basic Protocol 2: Exploring the Content of the ELM Database Using the General Search
  • Basic Protocol 3: Detecting Short Linear Motifs in Protein Sequences
  • Basic Protocol 4: Detecting Short Linear Motifs in Novel Protein Sequences
  • Basic Protocol 5: Searching the ELM Database Using the Rest API
  • Basic Protocol 6: Detecting Short Linear Motifs in Sequences Using the Rest API
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
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Key References
  Dinkel, H., Van Roey, K., Michael, S., Kumar, M., Uyar, B., Altenberg, B., … Gibson, T. J. (2016). ELM 2016‐data update and new functionality of the eukaryotic linear motif resource. Nucleic Acids Research, 44, D294–300. doi: 10.1093/nar/gkv1291.
  This is the latest publication on the ELM database highlighting the newest features.
  Gibson et al., 2015. See above.
  This guide is meant for experimentalists working on detecting/validating short linear motif instances.
  Davey et al., 2012. See above.
  This review summarizes the biochemical properties of short linear motifs.
  Van Roey et al., 2014. See above.
  Comprehensive review about short linear motifs with extensive biological examples.
Internet Resources
  Clustal Omega (Sievers et al., ) is a tool for the alignment of multiple nucleic acid and protein sequences.
  Jalview (Waterhouse et al., ) is a Java desktop application (and browser applet) that employs Web services for sequence alignment and visualization.
  ProViz (Jehl, Manguy, Shields, Higgins, & Davey, ) is an interactive protein exploration tool, which searches several databases for information about a given query protein. Data relevant to the protein, like an alignment of homologs, linear motifs, post‐translational modifications, domains, secondary structures, sequence variations, and others are graphically represented relative to their position in the protein.
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