**3. Materials and Methods**

3D-PP discovers conserved 3D protein patterns among an arbitrary set of structures uploaded by the user. For this, the user must define the following five threshold parameters:


The sites, each one defined as a structural arrangement of residues, form different structural clusters in the same 3D-pattern. Each cluster has a central feature named coverage (*Cv*), which represents the conservation level among the evaluated proteins. For example, a *Cv* value of 100% denotes a cluster formed by sites occurring in all the assessed proteins and whose structural orientation/conformation show high similarity. Detailed information about the architecture and the essential components of 3D-PP are shown in the Supplementary Data, Figure S5.
