iELM

iELM predicts the function and positional interface of short linear motifs (SLiMs) that mediate protein–protein interactions (PPIs) to annotate and analyze SLiM-mediated interactions within PPI networks.

Key Features:

• SLiM function and interface prediction: Predicts the functional role and positional molecular interface of SLiMs within PPIs.
• ELM-annotated SLiM classes: Utilizes annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource as the core annotation set.
• PPI network exploration and generation: Explores pre-existing annotated PPI networks and generates new PPI networks focused on SLiM-mediated interactions.
• Functional inference: Infers whether predicted SLiM-mediated interactions are associated with processes such as complex formation or degradation.
• Molecular interface data: Provides information on the molecular interface of SLiM-mediated interactions derived from sequence and annotation data.
• Annotation provenance: Incorporates annotations and modular architecture information from UniProt and Phospho.ELM for interpretation and visualization.
• Network contextualization: Produces network figures that contextualize predicted SLiM-mediated interactions within broader biological networks.
• Scalability: Supports analysis of single proteins and large-scale proteomic submissions.

Scientific Applications:

• Proteomic analysis: Enables proteome-wide identification and annotation of SLiM-mediated PPIs.
• PPI functional annotation: Facilitates assignment of functional roles to PPIs mediated by SLiMs, including complex assembly and degradation pathways.
• Network biology: Contextualizes SLiM-mediated interactions within interaction networks to support systems-level interpretations.
• SLiM-focused studies: Supports studies of SLiM prevalence, positional distribution, and contribution to protein modular architecture.

Methodology:

The core algorithm utilizes annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource, explores and generates SLiM-focused PPI networks, and incorporates UniProt and Phospho.ELM annotations for molecular interface and modular architecture information.