ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins - PubMed (original) (raw)
. 2003 Jul 1;31(13):3625-30.
doi: 10.1093/nar/gkg545.
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 Gudavalli, Ivica Letunic, Peer Bork, Leszek Rychlewski, Bernhard Küster, Manuela Helmer-Citterich, William N Hunter, Rein Aasland, Toby J Gibson
Affiliations
- PMID: 12824381
- PMCID: PMC168952
- DOI: 10.1093/nar/gkg545
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins
Pål Puntervoll et al. Nucleic Acids Res. 2003.
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.
Figures
Figure 1
Scheme of the ELM server flowthrough using human RASN as a query. Dashed boxes indicate the four stages from input to result. As the server is further developed, more filters will be added (light blue) requiring more query-dependent data to be retrievable (pink parallelograms).
Figure 2
Example of ELM server output using a short sequence, human RASN, as query. The output provides a table summarising the matches and the filtering, a list of globular domains revealed by the SMART server (in this case the RAS domain entry), the list of motif matches that survived filtering (in this case only the C-terminal prenylation site), and finally the list of matches excluded by domain filtering. Hyperlinks to the filtered results as well as to ELM annotation are provided.
Similar articles
- Fast and scalable querying of eukaryotic linear motifs with gget elm.
Luebbert L, Hoang C, Kumar M, Pachter L. Luebbert L, et al. Bioinformatics. 2024 Mar 4;40(3):btae095. doi: 10.1093/bioinformatics/btae095. Bioinformatics. 2024. PMID: 38377393 Free PMC article. - ELM: the status of the 2010 eukaryotic linear motif resource.
Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ. Gould CM, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. Epub 2009 Nov 17. Nucleic Acids Res. 2010. PMID: 19920119 Free PMC article. - A structure filter for the Eukaryotic Linear Motif Resource.
Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M. Via A, et al. BMC Bioinformatics. 2009 Oct 24;10:351. doi: 10.1186/1471-2105-10-351. BMC Bioinformatics. 2009. PMID: 19852836 Free PMC article. - DILIMOT: discovery of linear motifs in proteins.
Neduva V, Russell RB. Neduva V, et al. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W350-5. doi: 10.1093/nar/gkl159. Nucleic Acids Res. 2006. PMID: 16845024 Free PMC article. - Computational prediction of protein-protein interactions.
Obenauer JC, Yaffe MB. Obenauer JC, et al. Methods Mol Biol. 2004;261:445-68. doi: 10.1385/1-59259-762-9:445. Methods Mol Biol. 2004. PMID: 15064475 Review.
Cited by
- StrIDR: a database of intrinsically disordered regions of proteins with experimentally resolved structures.
Majila K, Viswanath S. Majila K, et al. bioRxiv [Preprint]. 2024 Aug 26:2024.08.22.609111. doi: 10.1101/2024.08.22.609111. bioRxiv. 2024. PMID: 39253485 Free PMC article. Preprint. - The astrovirus N-terminal nonstructural protein anchors replication complexes to the perinuclear ER membranes.
Ali H, Noyvert D, Hankinson J, Lindsey G, Lulla A, Lulla V. Ali H, et al. PLoS Pathog. 2024 Jul 15;20(7):e1011959. doi: 10.1371/journal.ppat.1011959. eCollection 2024 Jul. PLoS Pathog. 2024. PMID: 39008516 Free PMC article. - C16ORF70/MYTHO promotes healthy aging in C.elegans and prevents cellular senescence in mammals.
Franco-Romero A, Morbidoni V, Milan G, Sartori R, Wulff J, Romanello V, Armani A, Salviati L, Conte M, Salvioli S, Franceschi C, Buonomo V, Swoboda CO, Grumati P, Pannone L, Martinelli S, Jefferies HB, Dikic I, van der Laan J, Cabreiro F, Millay DP, Tooze SA, Trevisson E, Sandri M. Franco-Romero A, et al. J Clin Invest. 2024 Jun 13;134(15):e165814. doi: 10.1172/JCI165814. J Clin Invest. 2024. PMID: 38869949 Free PMC article. - Fast and scalable querying of eukaryotic linear motifs with gget elm.
Luebbert L, Hoang C, Kumar M, Pachter L. Luebbert L, et al. Bioinformatics. 2024 Mar 4;40(3):btae095. doi: 10.1093/bioinformatics/btae095. Bioinformatics. 2024. PMID: 38377393 Free PMC article. - Deep Learning in Phosphoproteomics: Methods and Application in Cancer Drug Discovery.
Varshney N, Mishra AK. Varshney N, et al. Proteomes. 2023 May 2;11(2):16. doi: 10.3390/proteomes11020016. Proteomes. 2023. PMID: 37218921 Free PMC article. Review.
References
- Kendrew J.C., Dickerson,R.E., Strandberg,B.E., Hart,R.G. and Davies,D.R. (1960) Structure of myoglobin A three-dimensional Fourier synthesis at 2 Å resolution. Nature, 185, 422–427. - PubMed
- Bang M.L., Centner,T., Fornoff,F., Geach,A.J., Gotthardt,M., McNabb,M., Witt,C.C., Labeit,D., Gregorio,C.C., Granzier,H. and Labeit,S. (2001) The complete gene sequence of titin, expression of an unusual approximately 700-kDa titin isoform, and its interaction with obscurin identify a novel Z-line to I-band linking system. Circ. Res., 89, 1065–1072. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources