iPfam is a resource that describes physical interactions between those Pfam domains that have a representative structure in the Protein DataBank (PDB). When two or more domains occur within a single structure, the domains are analysed to see if they form an interaction. If the domains are close enough to form an interaction, the bonds that play a role in that that interaction are determined.
Our goal has been to re-calculate iPfam interaction data for each new Pfam release, so that, as Pfam changes, the information within iPfam remains up to date. Unfortunately, we rely heavily on data from two other major biological databases, the PDB and UniProt. Specifically, in order to calculate our interaction data we require a mapping between residues in the PDB and UniProt and another mapping between UniProt and Pfam residues. Recently the PDB has undergone a major change, with the shift to remediated PDB files. This has required the generation of two entirely new mappings, which has been a significant, time-consuming undertaking.
We are now in the process of generating a new iPfam release and are developing a new website to house these data. Please bear with us as we bring iPfam back online. In the meantime, you can access iPfam data corresponding to Pfam release 21.0, via our FTP site.