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

References in zbMATH (referenced in 8 articles )

Showing results 1 to 8 of 8.
Sorted by year (citations)

  1. Carugo, Oliviero (ed.); Eisenhaber, Frank (ed.): Data mining techniques for the life sciences (2016)
  2. Basu, Subhadip; Plewczynski, Dariusz: AMS 3.0: prediction of post-translational modifications (2010) ioport
  3. Davey, Norman E.; Edwards, Richard J.; Shields, Denis C.: Estimation and efficient computation of the true probability of recurrence of short linear protein sequence motifs in unrelated proteins (2010) ioport
  4. Hu, Jianjun; Zhang, Fan: Bayesmotif: de novo protein sorting motif discovery from impure datasets (2010) ioport
  5. Via, Allegra; Gould, Cathryn M.; Gemünd, Christine; Gibson, Toby J.; Helmer-Citterich, Manuela: A structure filter for the eukaryotic linear motif resource (2009) ioport
  6. Dogruel, Mutlu; Down, Thomas A.; Hubbard, Tim J. P.: Nestedmica as an ab initio protein motif discovery tool (2008) ioport
  7. Mistry, Jaina; Bateman, Alex; Finn, Robert D.: Predicting active site residue annotations in the pfam database (2007) ioport
  8. 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 Stanislaw; 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. (2003) ioport