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 GudavalliIvica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N. Hunter, Rein Aasland, Toby J. Gibson*

*Corresponding author for this work

    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 - 1 Jul 2003

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

    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
    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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    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.",
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    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

    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

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    AU - Mattingsdal, Morten

    AU - Cameron, Scott

    AU - Martin, David M.A.

    AU - Ausiello, Gabriele

    AU - Brannetti, Barbara

    AU - Costantini, Anna

    AU - Ferrè, Fabrizio

    AU - Maselli, Vincenza

    AU - Via, Allegra

    AU - Cesareni, Gianni

    AU - Diella, Francesca

    AU - Superti-Furga, Giulio

    AU - Wyrwicz, Lucjan

    AU - Ramu, Chenna

    AU - McGuigan, Caroline

    AU - Gudavalli, Rambabu

    AU - Letunic, Ivica

    AU - Bork, Peer

    AU - Rychlewski, Leszek

    AU - Küster, Bernhard

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    AU - Gibson, Toby J.

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    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