title: ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
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.
authors.affiliation: Department of Molecular Biology, University of Bergen, Norway.
authors.forename: Pål
authors.initials: P
authors.lastname: Puntervoll
authors.forename: Rune
authors.initials: R
authors.lastname: Linding
authors.forename: Christine
authors.initials: C
authors.lastname: Gemünd
authors.forename: Sophie
authors.initials: S
authors.lastname: Chabanis-Davidson
authors.forename: Morten
authors.initials: M
authors.lastname: Mattingsdal
authors.forename: Scott
authors.initials: S
authors.lastname: Cameron
authors.forename: David M A
authors.initials: DM
authors.lastname: Martin
authors.forename: Gabriele
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authors.lastname: Ausiello
authors.forename: Barbara
authors.initials: B
authors.lastname: Brannetti
authors.forename: Anna
authors.initials: A
authors.lastname: Costantini
authors.forename: Fabrizio
authors.initials: F
authors.lastname: Ferrè
authors.forename: Vincenza
authors.initials: V
authors.lastname: Maselli
authors.forename: Allegra
authors.initials: A
authors.lastname: Via
authors.forename: Gianni
authors.initials: G
authors.lastname: Cesareni
authors.forename: Francesca
authors.initials: F
authors.lastname: Diella
authors.forename: Giulio
authors.initials: G
authors.lastname: Superti-Furga
authors.forename: Lucjan
authors.initials: L
authors.lastname: Wyrwicz
authors.forename: Chenna
authors.initials: C
authors.lastname: Ramu
authors.forename: Caroline
authors.initials: C
authors.lastname: McGuigan
authors.forename: Rambabu
authors.initials: R
authors.lastname: Gudavalli
authors.forename: Ivica
authors.initials: I
authors.lastname: Letunic
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Leszek
authors.initials: L
authors.lastname: Rychlewski
authors.forename: Bernhard
authors.initials: B
authors.lastname: Küster
authors.forename: Manuela
authors.initials: M
authors.lastname: Helmer-Citterich
authors.forename: William N
authors.initials: WN
authors.lastname: Hunter
authors.forename: Rein
authors.initials: R
authors.lastname: Aasland
authors.forename: Toby J
authors.initials: TJ
authors.lastname: Gibson
mesh_terms: D020816:Amino Acid Motifs; D005057:Eukaryotic Cells / Q000737:chemistry*; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000502:physiology; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D011506:Proteins