Bioinformatical detection of recognition factors for ubiquitin and SUMO

The specific recognition of ubiquitin, small ubiquitin-like modifier (SUMO), and related proteins is absolutely crucial for the signaling capacity of these modifiers. Most ubiquitin receptor proteins employ dedicated ubiquitin binding domains (UBDs), of which about 15 families have been described. By contrast, SUMO is recognized by short linear motifs that comprise only a few residues and do not require a defined tertiary structure. At the moment, three classes of SUMO-interacting motifs (SIMs) have been described. The recognition modes of most other modifiers remain poorly understood. When working with ubiquitin-family modifiers, a frequently occurring task is to assess a given protein sequence for the presence of known ubiquitin- or SUMO-binding elements. Due to the different nature of UBDs and SIMs, completely different approaches have to be used. This chapter addresses the bioinformatical detection of UBDs and SIMs through Web-based methods that are freely accessible and do not require a particular bioinformatics infrastructure.