Eukaryotic Linear Motif resource

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Descriptioneukaryotic linear motifs.
AuthorsHolger Dinkel
Toby Gibson
Primary citationDinkel & al. (2012)[1]
Release date2011

The Eukaryotic Linear Motif (ELM) resource is a computational biology resource (developed at the European Molecular Biology Laboratory (EMBL)) for investigating short linear motifs (SLiMs) in eukaryotic proteins.[2][3] It is currently the largest collection of linear motif classes with annotated and experimentally validated linear motif instances.

Linear motifs are specified as patterns using regular expression rules. These expressions are used in the ELM prediction pipeline which detects putative motif instances in protein sequences. To improve the predictive power, context-based rules and logical filters are being developed and applied to reduce the amount of false positives matches.

As of 2010 ELM contained 146 different motifs that annotate more than 1300 experimentally determined instances within proteins.[3] The current version of the ELM server provides filtering by cell compartment, phylogeny, globular domain clash (using the SMART/Pfam databases) and structure.[4] In addition, both the known ELM instances and any positionally conserved matches in sequences similar to ELM instance sequences are identified and displayed.

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  1. ^ Dinkel, Holger; Michael Sushama; Weatheritt Robert J; Davey Norman E; Van Roey Kim; Altenberg Brigitte; Toedt Grischa; Uyar Bora; Seiler Markus; Budd Aidan; Jödicke Lisa; Dammert Marcel A; Schroeter Christian; Hammer Maria; Schmidt Tobias; Jehl Peter; McGuigan Caroline; Dymecka Magdalena; Chica Claudia; Luck Katja; Via Allegra; Chatr-Aryamontri Andrew; Haslam Niall; Grebnev Gleb; Edwards Richard J; Steinmetz Michel O; Meiselbach Heike; Diella Francesca; Gibson Toby J (Jan 2012). "ELM--the database of eukaryotic linear motifs". Nucleic Acids Research. 40 (D1): D242–D251. doi:10.1093/nar/gkr1064. PMC 3245074. PMID 22110040.
  2. ^ Puntervoll P, Linding R, Gemünd C, et al. (July 2003). "ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins". Nucleic Acids Res. 31 (13): 3625–30. doi:10.1093/nar/gkg545. PMC 168952. PMID 12824381.
  3. ^ a b Gould CM, Diella F, Via A, et al. (January 2010). "ELM: the status of the 2010 eukaryotic linear motif resource". Nucleic Acids Res. 38 (Database issue): D167–80. doi:10.1093/nar/gkp1016. PMC 2808914. PMID 19920119.
  4. ^ Via A, Gould CM, Gemünd C, Gibson TJ, Helmer-Citterich M (2009). "A structure filter for the Eukaryotic Linear Motif Resource". BMC Bioinformatics. 10: 351. doi:10.1186/1471-2105-10-351. PMC 2774702. PMID 19852836.

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