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ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins

Puntervoll, P; Linding, R; Gemund, C; Chabanis-Davidson, S; Mattingsdal, M; Cameron, S; Martin, DM; ... Gibson, TJ; + view all (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research , 31 (13) 3625 - 3630. 10.1093/nar/gkg545. Green open access

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Abstract

Multidomain proteins predominate in eukaryotic proteomes. Individual functions assigned to different sequence segments combine to create a complex function for the whole protein. While on-line resources are available for revealing globular domains in sequences, there has hitherto been no comprehensive collection of small functional sites/motifs comparable to the globular domain resources, yet these are as important for the function of multidomain proteins. Short linear peptide motifs are used for cell compartment targeting, protein-protein interaction, regulation by phosphorylation, acetylation, glycosylation and a host of other post-translational modifications. ELM, the Eukaryotic Linear Motif server at http://elm.eu.org/, is a new bioinformatics resource for investigating candidate short non-globular functional motifs in eukaryotic proteins, aiming to fill the void in bioinformatics tools. Sequence comparisons with short motifs are difficult to evaluate because the usual significance assessments are inappropriate. Therefore the server is implemented with several logical filters to eliminate false positives. Current filters are for cell compartment, globular domain clash and taxonomic range. In favourable cases, the filters can reduce the number of retained matches by an order of magnitude or more.

Type: Article
Title: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
Open access status: An open access version is available from UCL Discovery
DOI: 10.1093/nar/gkg545
Publisher version: http://dx.doi.org/10.1093/nar/gkg545
Language: English
Additional information: This is an Oxford Journals Open Access article.
Keywords: *Amino Acid Motifs Eukaryotic Cells/*chemistry Internet Protein Structure, Tertiary Proteins/chemistry/physiology Sequence Analysis, Protein/*methods *Software User-Computer Interface
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio
URI: https://discovery.ucl.ac.uk/id/eprint/1307454
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