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PMID: 24214962 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The eukaryotic linear motif resource ELM: 10 years and counting.

Nucleic acids research ·Vol. 42 ·No. Database issue ·2014-01-00 ·Pages D259-66

Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Krüger D, Grebnev G, Kuban M, Strumillo M, Uyar B, Budd A, Altenberg B, Seiler M, Chemes LB, Glavina J, Sánchez IE, Diella F, Gibson TJ

Abstract

The eukaryotic linear motif (ELM http://elm.eu.org) resource is a hub for collecting, classifying and curating information about short linear motifs (SLiMs). For >10 years, this resource has provided the scientific community with a freely accessible guide to the biology and function of linear motifs. The current version of ELM contains ∼200 different motif classes with over 2400 experimentally validated instances manually curated from >2000 scientific publications. Furthermore, detailed information about motif-mediated interactions has been annotated and made available in standard exchange formats. Where appropriate, links are provided to resources such as switches.elm.eu.org and KEGG pathways.

MeSH Terms
Amino Acid Motifs Databases, Protein Internet Multiprotein Complexes/chemistry Protein Interaction Domains and Motifs
Chemicals
Multiprotein Complexes
Authors & Affiliations
20 authors, click to expand affiliations / ORCID
Dinkel Holger
Structural and Computational Biology, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany, Department of Physiology, University of California, San Francisco, 600 16th Street, San Francisco, CA 94158, USA, Structural Studies Division, MRC, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK, Ruprecht-Karls-Universität, 69117 Heidelberg, Germany, School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Co. Dublin, Republic of Ireland, Laboratory of Bioinformatics and Biostatistics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland, Protein Structure-Function and Engineering Laboratory, Fundación Instituto Leloir and Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas Avenida Patricias Argentinas 435 CP 1405 Buenos Aires, Argentina and Departamento de Química Biológica and IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Gúiraldes 2160 CP 1428, Argentina.
Van Roey Kim
Michael Sushama
Davey Norman E
Weatheritt Robert J
Born Diana
Speck Tobias
Krüger Daniel
Grebnev Gleb
Kuban Marta
Strumillo Marta
Uyar Bora
Budd Aidan
Altenberg Brigitte
Seiler Markus
Chemes Lucía B
Glavina Juliana
Sánchez Ignacio E
Diella Francesca
Gibson Toby J
References (50)
50 references, click to expand
  1. Targeting proteins for degradation.
    Nat Chem Biol. 2009 Nov;5(11):815-22 PMID: 19841631
  2. ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins.
    Nucleic Acids Res. 2003 Jul 1;31(13):3625-30 PMID: 12824381
  3. Mammalian Cdh1/Fzr mediates its own degradation.
    EMBO J. 2004 Apr 7;23(7):1619-26 PMID: 15029244
  4. iELM--a web server to explore short linear motif-mediated interactions.
    Nucleic Acids Res. 2012 Jul;40(Web Server issue):W364-9 PMID: 22638578
  5. Cdc20 mediates D-box-dependent degradation of Sp100.
    Biochem Biophys Res Commun. 2011 Dec 2;415(4):702-6 PMID: 22086178
  6. Protein disorder and short conserved motifs in disordered regions are enriched near the cytoplasmic side of single-pass transmembrane proteins.
    PLoS One. 2012;7(9):e44389 PMID: 22962613
  7. Docking interactions in protein kinase and phosphatase networks.
    Curr Opin Struct Biol. 2006 Dec;16(6):676-85 PMID: 17079133
  8. Measurement of the binding of tyrosyl phosphopeptides to SH2 domains: a reappraisal.
    Proc Natl Acad Sci U S A. 1995 Apr 11;92(8):3199-203 PMID: 7536927
  9. Acm1 is a negative regulator of the CDH1-dependent anaphase-promoting complex/cyclosome in budding yeast.
    Mol Cell Biol. 2006 Dec;26(24):9162-76 PMID: 17030612
  10. Why are "natively unfolded" proteins unstructured under physiologic conditions?
    Proteins. 2000 Nov 15;41(3):415-27 PMID: 11025552
  11. Local structural disorder imparts plasticity on linear motifs.
    Bioinformatics. 2007 Apr 15;23(8):950-6 PMID: 17387114
  12. SMART 7: recent updates to the protein domain annotation resource.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D302-5 PMID: 22053084
  13. Structural and functional characterization of the protein kinase Mps1 in Arabidopsis thaliana.
    PLoS One. 2012;7(9):e45707 PMID: 23049844
  14. New structural and functional contexts of the Dx[DN]xDG linear motif: insights into evolution of calcium-binding proteins.
    PLoS One. 2011;6(6):e21507 PMID: 21720552
  15. Computational modelling of linear motif-mediated protein interactions.
    Curr Top Med Chem. 2012;12(14):1553-61 PMID: 22827524
  16. Doc1 mediates the activity of the anaphase-promoting complex by contributing to substrate recognition.
    EMBO J. 2003 Feb 17;22(4):786-96 PMID: 12574115
  17. The transience of transient overexpression.
    Nat Methods. 2013 Aug;10(8):715-21 PMID: 23900254
  18. Attributes of short linear motifs.
    Mol Biosyst. 2012 Jan;8(1):268-81 PMID: 21909575
  19. Viral infection and human disease--insights from minimotifs.
    Front Biosci. 2008 May 01;13:6455-71 PMID: 18508672
  20. UCSF Chimera--a visualization system for exploratory research and analysis.
    J Comput Chem. 2004 Oct;25(13):1605-12 PMID: 15264254
  21. Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.
    BMC Biol. 2007 Oct 09;5:44 PMID: 17925023
  22. Cyclin is degraded by the ubiquitin pathway.
    Nature. 1991 Jan 10;349(6305):132-8 PMID: 1846030
  23. Intrinsically unstructured proteins and their functions.
    Nat Rev Mol Cell Biol. 2005 Mar;6(3):197-208 PMID: 15738986
  24. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.
    Bioinformatics. 2008 Feb 15;24(4):453-7 PMID: 18184688
  25. Structures of APC/C(Cdh1) with substrates identify Cdh1 and Apc10 as the D-box co-receptor.
    Nature. 2011 Feb 10;470(7333):274-8 PMID: 21107322
  26. The processivity of multiubiquitination by the APC determines the order of substrate degradation.
    Cell. 2006 Jan 13;124(1):89-103 PMID: 16413484
  27. Molecular principles of the interactions of disordered proteins.
    J Mol Biol. 2007 Sep 14;372(2):549-61 PMID: 17681540
  28. ELM--the database of eukaryotic linear motifs.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D242-51 PMID: 22110040
  29. Motif switches: decision-making in cell regulation.
    Curr Opin Struct Biol. 2012 Jun;22(3):378-85 PMID: 22480932
  30. Unique D box and KEN box sequences limit ubiquitination of Acm1 and promote pseudosubstrate inhibition of the anaphase-promoting complex.
    J Biol Chem. 2008 Aug 29;283(35):23701-10 PMID: 18596038
  31. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.
    J Mol Biol. 1999 Oct 22;293(2):321-31 PMID: 10550212
  32. KEGG-based pathway visualization tool for complex omics data.
    In Silico Biol. 2005;5(4):419-23 PMID: 16268787
  33. A novel hepacivirus with an unusually long and intrinsically disordered NS5A protein in a wild Old World primate.
    J Virol. 2013 Aug;87(16):8971-81 PMID: 23740998
  34. Intrinsically disordered proteins: a 10-year recap.
    Trends Biochem Sci. 2012 Dec;37(12):509-16 PMID: 22989858
  35. Dephosphorylation of Cdc20 is required for its C-box-dependent activation of the APC/C.
    EMBO J. 2012 Aug 1;31(15):3351-62 PMID: 22713866
  36. Exploring the diversity of SPRY/B30.2-mediated interactions.
    Trends Biochem Sci. 2013 Jan;38(1):38-46 PMID: 23164942
  37. The KEN box: an APC recognition signal distinct from the D box targeted by Cdh1.
    Genes Dev. 2000 Mar 15;14(6):655-65 PMID: 10733526
  38. Understanding eukaryotic linear motifs and their role in cell signaling and regulation.
    Front Biosci. 2008 May 01;13:6580-603 PMID: 18508681
  39. Peptide-binding domains: are limp handshakes safest?
    Sci Signal. 2012 Sep 25;5(243):pe40 PMID: 23012652
  40. The Pfam protein families database.
    Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301 PMID: 22127870
  41. The switches.ELM resource: a compendium of conditional regulatory interaction interfaces.
    Sci Signal. 2013 Apr 02;6(269):rs7 PMID: 23550212
  42. The anaphase promoting complex/cyclosome: a machine designed to destroy.
    Nat Rev Mol Cell Biol. 2006 Sep;7(9):644-56 PMID: 16896351
  43. Linear motifs: evolutionary interaction switches.
    FEBS Lett. 2005 Jun 13;579(15):3342-5 PMID: 15943979
  44. How viruses hijack cell regulation.
    Trends Biochem Sci. 2011 Mar;36(3):159-69 PMID: 21146412
  45. REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock.
    PLoS Genet. 2011 Mar;7(3):e1001350 PMID: 21483796
  46. The emerging contribution of sequence context to the specificity of protein interactions mediated by PDZ domains.
    FEBS Lett. 2012 Aug 14;586(17):2648-61 PMID: 22709956
  47. PepSite: prediction of peptide-binding sites from protein surfaces.
    Nucleic Acids Res. 2012 Jul;40(Web Server issue):W423-7 PMID: 22600738
  48. ELM: the status of the 2010 eukaryotic linear motif resource.
    Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80 PMID: 19920119
  49. Intrinsically disordered protein.
    J Mol Graph Model. 2001;19(1):26-59 PMID: 11381529
  50. Capturing cooperative interactions with the PSI-MI format.
    Database (Oxford). 2013 Sep 25;2013:bat066 PMID: 24067240
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkt1047
Published
2014-01-00
Epub
2013-00-07
Pages
D259-66
Language
English
Region
England
NLM ID
0411011
PMCID
PMC3964949
Subset
IM
Grants
Medical Research Council · MC_U105185859 · United Kingdom
Medical Research Council · U105185859 · United Kingdom
External Links
PubMed source DOI: 10.1093/nar/gkt1047 PMC Full Text View journal details
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