ELM: the status of the 2010 eukaryotic linear motif resource.
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Date
2010-01-01ICR Author
Author
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
Type
Journal Article
Metadata
Show full item recordAbstract
Linear motifs are short segments of multidomain proteins that provide regulatory functions independently of protein tertiary structure. Much of intracellular signalling passes through protein modifications at linear motifs. Many thousands of linear motif instances, most notably phosphorylation sites, have now been reported. Although clearly very abundant, linear motifs are difficult to predict de novo in protein sequences due to the difficulty of obtaining robust statistical assessments. The ELM resource at http://elm.eu.org/ provides an expanding knowledge base, currently covering 146 known motifs, with annotation that includes >1300 experimentally reported instances. ELM is also an exploratory tool for suggesting new candidates of known linear motifs in proteins of interest. Information about protein domains, protein structure and native disorder, cellular and taxonomic contexts is used to reduce or deprecate false positive matches. Results are graphically displayed in a 'Bar Code' format, which also displays known instances from homologous proteins through a novel 'Instance Mapper' protocol based on PHI-BLAST. ELM server output provides links to the ELM annotation as well as to a number of remote resources. Using the links, researchers can explore the motifs, proteins, complex structures and associated literature to evaluate whether candidate motifs might be worth experimental investigation.
Collections
Subject
Amino Acid Motifs
Amino Acid Sequence
Animals
Computational Biology
Databases, Genetic
Databases, Nucleic Acid
Databases, Protein
Eukaryotic Cells
Humans
Information Storage and Retrieval
Internet
Molecular Sequence Data
Protein Structure, Tertiary
Sequence Homology, Amino Acid
Software
Language
eng
License start date
2010-01
Citation
Nucleic Acids Res, 2010, 38 (Database issue), pp. D167 - D180
Publisher
OXFORD UNIV PRESS