Fig. 1: The infrastructure of the ProtCID web site.

There are four types of queries that can be input by users: a PDB ID; one or two Pfam IDs; one or two sequences; and one or more UniProt IDs. The user can also browse all available Pfam IDs, Clan IDs, Pfam–Pfam pairs, peptide-interacting Pfams, and ligands. A Pfam page provides a list of PDB structures containing the Pfam. Clicking on one structure leads to the same page as querying by that PDB ID, which shows the Pfam architecture of the entry. From the PDB entry page, a user can select and display interface clusters: chain–chain interfaces, domain–domain interfaces, as well as domain–peptide interfaces. The coordinates of different interactions and clusters can be downloaded from the Pfam pages and the cluster pages.