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

    477 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

    Fingerprint Dive into the research topics of 'ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins'. Together they form a unique fingerprint.

  • Cite this

    Puntervoll, P., Linding, R., Gemünd, C., Chabanis-Davidson, S., Mattingsdal, M., Cameron, S., Martin, D. M. A., 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., ... 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