SLiMAn 2.0: meaningful navigation through peptide-protein interaction networks

Among the myriad of protein-protein interactions occurring in living organisms, a substantial amount involves small linear motifs (SLiMs) recognized by structured domains. However, predictions of SLiM-based networks are tedious, due to the abundance of such motifs and a high portion of false positive hits. For this reason, a webserver SLiMAn (Short Linear Motif Analysis) was developed to focus the search on the most relevant SLiMs. Using SLiMAn, one can navigate into a given (meta-)interactome and tune a variety of parameters associated to each type of SLiMs in attempt to identify functional ELM motifs and their recognition domains. The IntAct and BioGRID databases bring experimental information, while IUPred and AlphaFold provide boundaries of folded and disordered regions. Post-translational modifications listed in PhosphoSite+ are highlighted. Links to PubMed accelerate scrutiny into the literature, to support (or not) putative pairings. Dedicated visualization features are also incorporated, such as Cytoscape for macromolecular networks and BINANA for intermolecular contacts within structural models generated by SCWRL 3.0. The use of SLiMAn 2.0 is illustrated on a simple example. It is freely available at https://sliman2.cbs.cnrs.fr.