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.
Puntervoll
Pål
P
Department of Molecular Biology, University of Bergen, Norway.
Linding
Rune
R
Gemünd
Christine
C
Chabanis-Davidson
Sophie
S
Mattingsdal
Morten
M
Cameron
Scott
S
Martin
David M A
DM
Ausiello
Gabriele
G
Brannetti
Barbara
B
Costantini
Anna
A
Ferrè
Fabrizio
F
Maselli
Vincenza
V
Via
Allegra
A
Cesareni
Gianni
G
Diella
Francesca
F
Superti-Furga
Giulio
G
Wyrwicz
Lucjan
L
Ramu
Chenna
C
McGuigan
Caroline
C
Gudavalli
Rambabu
R
Letunic
Ivica
I
Bork
Peer
P
Rychlewski
Leszek
L
Küster
Bernhard
B
Helmer-Citterich
Manuela
M
Hunter
William N
WN
Aasland
Rein
R
Gibson
Toby J
TJ
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
D011506:Proteins