ELM server

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

Pål Puntervoll, Rune Linding, Christine Gemünd, Sophie Chabanis-Davidson, Morten Mattingsdal, Scott Cameron, David M A Martin, Gabriele Ausiello, Barbara Brannetti, Anna Costantini, Fabrizio Ferrè, Vincenza Maselli, Allegra Via, Gianni Cesareni, Francesca Diella, Giulio Superti-Furga, Lucjan Wyrwicz, Chenna Ramu, Caroline McGuigan, Rambabu Gudavalli & 8 others Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson

Research output: Contribution to journalArticle

471 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3625-3630
Number of pages6
JournalNucleic Acids Research
Volume31
Issue number13
DOIs
Publication statusPublished - Jul 1 2003

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Proteins
Computational Biology
Protein Transport
Proteome
Post Translational Protein Processing
Acetylation
Glycosylation
Phosphorylation
Peptides

ASJC Scopus subject areas

  • Genetics

Cite this

Puntervoll, P., Linding, R., Gemünd, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., ... Gibson, T. J. (2003). ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research, 31(13), 3625-3630. https://doi.org/10.1093/nar/gkg545

ELM server : A new resource for investigating short functional sites in modular eukaryotic proteins. / Puntervoll, Pål; Linding, Rune; Gemünd, Christine; Chabanis-Davidson, Sophie; Mattingsdal, Morten; Cameron, Scott; Martin, David M A; Ausiello, Gabriele; Brannetti, Barbara; Costantini, Anna; Ferrè, Fabrizio; Maselli, Vincenza; Via, Allegra; Cesareni, Gianni; Diella, Francesca; Superti-Furga, Giulio; Wyrwicz, Lucjan; Ramu, Chenna; McGuigan, Caroline; Gudavalli, Rambabu; Letunic, Ivica; Bork, Peer; Rychlewski, Leszek; Küster, Bernhard; Helmer-Citterich, Manuela; Hunter, William N.; Aasland, Rein; Gibson, Toby J.

In: Nucleic Acids Research, Vol. 31, No. 13, 01.07.2003, p. 3625-3630.

Research output: Contribution to journalArticle

Puntervoll, P, Linding, R, Gemünd, C, Chabanis-Davidson, S, Mattingsdal, M, Cameron, S, Martin, DMA, Ausiello, G, Brannetti, B, Costantini, A, Ferrè, F, Maselli, V, Via, A, Cesareni, G, Diella, F, Superti-Furga, G, Wyrwicz, L, Ramu, C, McGuigan, C, Gudavalli, R, Letunic, I, Bork, P, Rychlewski, L, Küster, B, Helmer-Citterich, M, Hunter, WN, Aasland, R & Gibson, TJ 2003, 'ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins', Nucleic Acids Research, vol. 31, no. 13, pp. 3625-3630. https://doi.org/10.1093/nar/gkg545
Puntervoll P, Linding R, Gemünd C, Chabanis-Davidson S, Mattingsdal M, Cameron S et al. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research. 2003 Jul 1;31(13):3625-3630. https://doi.org/10.1093/nar/gkg545
Puntervoll, Pål ; Linding, Rune ; Gemünd, Christine ; Chabanis-Davidson, Sophie ; Mattingsdal, Morten ; Cameron, Scott ; Martin, David M A ; Ausiello, Gabriele ; Brannetti, Barbara ; Costantini, Anna ; Ferrè, Fabrizio ; Maselli, Vincenza ; Via, Allegra ; Cesareni, Gianni ; Diella, Francesca ; Superti-Furga, Giulio ; Wyrwicz, Lucjan ; Ramu, Chenna ; McGuigan, Caroline ; Gudavalli, Rambabu ; Letunic, Ivica ; Bork, Peer ; Rychlewski, Leszek ; Küster, Bernhard ; Helmer-Citterich, Manuela ; Hunter, William N. ; Aasland, Rein ; Gibson, Toby J. / ELM server : A new resource for investigating short functional sites in modular eukaryotic proteins. In: Nucleic Acids Research. 2003 ; Vol. 31, No. 13. pp. 3625-3630.
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