The interactions of Eukaryotic Linear Motif (iELM) web server facilitates the exploration of short linear motif- (SLiM) mediated interfaces within protein–protein interaction (PPI) networks (1). The importance of SLiMs in the regulatory and signalling mechanisms of the cell is becoming increasingly apparent, as highlighted by their use as molecular switches coordinating phase transitions in the cell (2) and their increasing association with disease (3–5). SLiMs are key components in a wide range of biological pathways and are known to act as sites for post-translational modifications such as phosphorylation or ubiquitination, as targeting signals for particular subcellular locations and as ligand-binding sites for protein recruitment (6,7). The majority of known motifs bind onto the surface of globular domains and exhibit specificity for a particular subgroup of a domain family (1). SLiMs tend to be just 3–10 amino acids in length with only 2–5 residues responsible for the majority of the binding affinity and specificity (6). This means that discriminating bioinformatically between a stochastic match and a result of biological relevance is fraught with difficulties (8).

The iELM algorithm has been previously described and benchmarked (1) and can be summarized as follows: iELM assesses binary protein associations for SLiM-mediated interactions using the ELM annotated regular expressions together with HMMs (26) trained on manually annotated SLiM-binding domains and their orthologs. The assessment of whether or not a binary interaction is SLiM-mediated can be divided into four sections. The first module uses the 3DID database (27) to check if the two proteins interact via a domain–domain interaction. If they do not, the second and third parts occur simultaneously to assess each protein for SLiM and SLiM-binding domain matches. In the second part, SLiMs are identified using the regular expressions annotated by the ELM resource, and scored using the SLiMSearch algorithm (12) based on the conservation of the motif in a multiple sequence alignment of the queried protein and its orthologs (12). The predicted SLiM and its surrounding amino acids are also assessed by the IUPred algorithm (14) for their propensity to be in a region of intrinsic disorder (14). In the third part, SLiM-binding domains are identified by HMMs trained to recognize SLiM-binding domains using the HMMSearch programme (26). An option is also available to search using Pfam HMMs (28); however, these domains do not take into account the specificity of motifs for subgroups of a domain family. If a complementary SLiM and SLiM-binding domain partnership exists within the two associated proteins, the algorithm uses a cut-off system based on the results from the benchmarking data sets (see Supplementary Figure S1), as well as recommendations present in the respective papers (1,12,14). The respective cut-offs are 0.3 for disorder scores, 0.6 for motifs scores and 0.35 for domain scores. Any scores below these values will not be returned by the web server.

The iELM web server is freely available at http://i.elm.eu.org with no login required. The server aims to provide a user-friendly interface for exploring a protein or proteome of interest for SLiM-mediated interactions. The server can be queried in two ways: ‘protein iELM’ searches the precalculated high-quality associations (score >0.6) from the STRING resource for SLiM-mediated interactions, whereas ‘proteomic iELM’ allows users to explore their own protein–protein interactome of interest for SLiMs. The server also provides a list of all 835 annotated linear motif-binding domains that can be freely downloaded at http://i.elm.eu.org/domains.

EMBL international PhD program fellowship to R.J.W. Funding for open access charge: EMBL.