
PDB-Structure 1JBAshowing a peptide from ELM classMOD_NMyristoyl
COVID-19 SLiM Links
HSTalks interview Gibson and Yamauchi on SARS-CoV-2 entry SLiMs
Our article on SLiM signatures in the SARS-CoV-2 entry system is now available at Science Signaling
Validation experiments for SARS-CoV-2 entry system SLiMs
SPIKE CendR and NRP1 Receptor in SARS-CoV-2 cell entry
SPIKE RGD and Integrin Receptors
- ELM database updates
The instances for ELM class LIG_FZD_DVL_PDZ have been added in the database. ELM class LIG_SH2_GRB2 has been changed to LIG_SH2_GRB2like, motif has been revised and several new instances for the same have been included.
- ELM database update
Two new classes added
LIG_NRP_CendR_1
LIG_PCNA_TLS_4
- ELM database update
Three new classes added
LIG_PCNA_yPIPBox_3
DOC_PP4_MxPP_1
DOC_PP4_FxxP_1
- ELM database update
Four new classes inserted
LIG_SH2_STAP1
LIG_SH2_NCK_1
LIG_PCNA_APIM_2
LIG_ARL_BART_1
Additionally, we have revised four other ELM classes
LIG_PCNA_PIPBox_1
LIG_Vh1_VBS_1
LIG_IRF3_LxIS_1
LIG_LIR_Gen_1
- ELM database updates
In a major update, more than 60 bacterial effector instances belonging to 20 different ELM motif classes have been added. Additionally, the Casein kinases - MOD_CK1_1 and MOD_CK2_1 have also been updated with 49 new instances.
- ELM database updates
The following new ELM classes have been integrated into the database:
MOD_DYRK1A_RPxSP_1
LIG_SH2_CRK
LIG_CaM_NSCaTE_8
MOD_PRMT_GGRGG_1
- ELM database updates
New ELM classes and their instances have been added:
LIG_deltaCOP1_diTrp_1
LIG_FXI_DFP_1
LIG_MLH1_MIPbox_1
TRG_Pf-PMV_PEXEL_1
Become an ELM sponsor?
The ELM phosphorylation DB
The Switches.ELM DB
Download a movie about a molecular switch involved in the formation of the ALG2/Alix complex
Welcome to the Eukaryotic Linear Motif (ELM) resource
This computational biology resource mainly focuses on annotation and detection of eukaryotic linear motifs (ELMs) by providing both a repository of annotated motif data and an exploratory tool for motif prediction. ELMs, or short linear motifs (SLiMs), are compact protein interaction sites composed of short stretches of adjacent amino acids. They are enriched in intrinsically disordered regions of the proteome and provide a wide range of functionality to proteins (Davey,2011,Van Roey,2014) They play crucial roles in cell regulation and are also of clinical importance, as aberrant SLiM function has been associated with several diseases and SLiM mimics are often used by pathogens to manipulate their hosts' cellular machinery (Davey,2011, Uyar,2014)
ELM Prediction
The ELM prediction tool scans user-submitted protein sequences for matches to the regular expressions defined in ELM. Distinction is made between matches that correspond to experimentally validated motif instances already curated in the ELM database and matches that correspond to putative motifs based on the sequence. Since SLiMs are short and degenerate, overprediction is likely and many putative SLiMs will be false positives. However, predictive power is improved by using additional filters based on contextual information, including taxonomy, cellular compartment, evolutionary conservation and structural features.
ELM DB
The ELM relational database stores different types of data about experimentally validated SLiMs that are manually curated from the literature. ELM instances are classified by motif type, functional site and ELM class. A functional site contains one to many ELM classes, which are described by a regular expression and list experimentally validated motif instances matching this sequence pattern. All data curated in ELM DB can be searched on the ELM website according to the following categories:
- 291 annotated ELM classes
- 3,542 experimentally validated ELM instances in 235 taxons
- 137 ELM methods described in 3,559 articles to experimentally validate ELM instances
- 527 solved PDB structures for curated ELM instances (from PDB)
- 147 globular ELM binding domains (from Pfam, SMART, and InterPro)
- 1,781 interactions mediated by curated ELM instances
- 887 regulatory switches mediated by curated ELM instances (from Switches.ELM DB)
- 784 pathways from KEGG involving linear motifs annotated in 832 Sequences
- 255 viral instances interfering with host cellular processes
- 11 ELM related diseases annotated as being caused by aberrant motif function
- 2 examples where pathogens abuse motifs to deregulate host cells
ELM Candidates
The ELM candidates pages contain lists of candidate classes and instances awaiting curation, and can be extended by users: Anybody can submit candidates, please provide as much information as possible. If you're interested in annotating a full ELM entry or individual instances, get in contact with the ELM team for procedures and awards!
ELM Information
The ELM information pages provide additional details to assist users in searching data in the ELM DB and in searching for putative motifs in query sequences. The Help page explains the use of regular expressions to define sequence patterns of ELM classes and to detect putative motifs in user-submitted query sequences, describes the filters that are applied to increase the reliability of the prediction tool, and defines terms frequently used in the ELM resource. The News lists changes and updates made to ELM, while the Links page lists links to other interesting bioinformatics resources. Funding information, participating groups and a list of ELM-related publications can be found on the About page.
ELM Downloads
Data curated in ELM DB can be downloaded and distributed for non-commercial use according to the ELM Software License Agreement.
ELM API
The ELM prediction tool can also be accessed programmatically via the ELM API. Read the API manual for more information.
Disclaimer
Short patterns applied to proteins are usually not statistically significant: Therefore we can't provide E-values as with BLAST searches. This means that most matches shown are more likely to be false positives than true matches. We hope that ELM server results will prove useful as guides to experimentation but they should not be treated as factual findings.
ELM data can be downloaded & distributed for non-commercial use according to the ELM Software License Agreement