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The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins

Francesca Diella¹, Allegra Via², Claudia Chica¹, Katja Luck³, Catherin M. Gould¹ & Toby J. Gibson¹

Correspondence: (Login to view email address)

1. Structural and Computational Biology, EMBL, Germany
2. Biocomputing Group, University of Rome "La Sapienza", Rome
3. Equipe Oncoproteines, EBSB, France

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Document Type:

Poster

Date:

Received 23 April 2009 10:26 UTC; Posted 23 April 2009

Subjects:

Bioinformatics

Tags:

• disorder
• sequence
• Evolution
• linear motif
• functional motifs
• Eukaryotic Linear Motif Resource
• annotation
• eukaryotes
• protein
• database
• ELM
• motifs

Abstract:

Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.

Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive over-prediction.

The Eukaryotic Linear Motif resource (ELM – http://elm.eu.org) is a bioinformatics facility for investigating candidate short functional motifs in eukaryotic proteins. The ELM database to date has collected more than 140 motifs and their regular expressions patterns as well as information about their instances of occurrence, distribution, crystal structure, publications, etc.

In order to reduce the over-prediction inherent to pattern matching against protein sequences and to discriminate true from false positive motif matches, context-based rules and logical filters are applied. The current version includes cell compartment, phylogeny, globular domain clash filters and the more recent structural filter based on known three-dimensional information that relies on structural information, such as residue solvent accessibility and secondary structure features. This implies that a candidate motif can be excluded from further consideration if the protein resides in the wrong cellular compartment or the motif is buried in the core of a globular domain.

By considering additional types of context information, we expect that prediction of functional sites by ELM can be considerably improved. In cases where the user cannot provide relevant context information, we consider providing predictions of contextual information in order to improve the ELM performance. For example, since the ELM motif database has been annotated with biological process GO terms, the system could be prepared for addition of a new context filter using biological process.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Diella, Francesca, Via, Allegra, Chica, Claudia, Luck, Katja, Gould, Catherin, and Gibson, Toby. The Eukaryotic Linear Motif Resource (ELM): Regulatory Sites in Proteins. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3152.1> (2009)

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