A fast way to discover new linear motifs

Welcome to LMD2 - the next generation of linear motif discovery. This tool takes protein sequences or interactions as input and determines the set of over-represented short sequence motifs present, scoring them according to over-representation, ortholog conservation, presense of motif-like residues, fit onto interacting partner surface (PepSite2) and how repeated the motif is within interacting partners. These scores are combined by a Bayesian integration approach, which was previously benchmarked on the ELM database to give estimates for False Positive Rate (FPR).