The switches.ELM resource

Short linear motifs (SLiMs) are compact, degenerate protein interaction interfaces that predominantly occur in intrinsically disordered protein regions (IDRs). Their intrinsic properties enable them to function as regulatory modules that can mediate switching between distinct functional states of a protein, which allows for context-dependent, integrative regulatory decision-making (Davey et al., 2012) (Van Roey et al., 2012). The switches.ELM database curates experimentally validated motif-based molecular switches, thereby providing a valuable collection of regulatory data that were dispersed in literature. In addition, based on these validated instances, the switches.ELM prediction tool was developed to identify possible switching mechanisms that might regulate a motif-containing protein of interest. Based on the underlying mechanisms, different types and subtypes of motif-based molecular switches were defined, an overview of which can be found on the 'Switch types' page.
The switches.ELM resource was curated and developed by the ELM consortium at the Gibson Team, EMBL Heidelberg.
Download a movie about a molecular switch involved in the formation of the ALG2/Alix complex:

References

switches.ELM

The switches.ELM Resource: A Compendium of Conditional Regulatory Interaction Interfaces. Van Roey et al., 2013

Further reading

• Motif switches: decision-making in cell regulation. Van Roey et al., 2012
• ELM--the database of eukaryotic linear motifs. Dinkel et al., 2012
• Attributes of short linear motifs. Davey et al., 2012
• A dynamic view of domain-motif interactions. Akiva et al., 2012
• How viruses hijack cell regulation. Davey et al., 2011
• Intrinsically disordered proteins: regulation and disease. Babu et al., 2011
• Protein binding specificity versus promiscuity. Schreiber et al., 2011
• Transient protein-protein interactions: structural, functional, and network properties. Perkins et al., 2010
• Protein dynamics and conformational disorder in molecular recognition. Mittag et al., 2010
• Post-translational modifications in signal integration. Deribe et al., 2010
• Cell regulation: determined to signal discrete cooperation. Gibson, 2009
• Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Diella et al., 2008
• Linear motifs: evolutionary interaction switches. Neduva et al., 2005

External data resources / tools

IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Dosztányi et al., 2005
The Pfam protein families database. Punta et al., 2012
Phospho.ELM: a database of phosphorylation sites--update 2011. Dinkel et al., 2011
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Hornbeck et al., 2012
SMART 6: recent updates and new developments. Letunic et al., 2009
ELM--the database of eukaryotic linear motifs. Dinkel et al., 2012
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Ashburner et al., 2000
Chemical Entities of Biological Interest: an update. de Matos et al., 2010
The European Nucleotide Archive. Leinonen et al., 2011
InterPro in 2011: new developments in the family and domain prediction database. Hunter et al., 2012
Reorganizing the protein space at the Universal Protein Resource (UniProt). Apweiler et al., 2012
The IntAct molecular interaction database in 2012. Kerrien et al., 2012
The Protein Data Bank. Berman et al., 2000
Reactome: a database of reactions, pathways and biological processes. Croft et al., 2011
Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. Kerrien et al., 2007

Acknowledgements

The switches.ELM resource is supported by:

the Systems Biology of Stem Cells and Reprogramming (SyBoSS, No. 242129) grant from the EU-EC Seventh Research Framework Programme (FP7)
the Eukaryotic Linear Motif (ELM) consortium
the European Molecular Biology Laboratory (EMBL)