There are three main entry points to the iPfam data: a protein family, a ligand or a protein structure. At the top of every page is a navigation bar that provides links to the home page, browse pages, FTP site and help sections. A page is typically broken down into a series of tabs that present the different data sections available.
Where appropriate in the site, we present an information box that summarizes the content of a section at a glance. This information box, if present, is located below the keyword search, on the top, right side of the page, and will always contain three icons indicating the number of domain-domain interactions, number of domain-ligand interactions and number of structures cited in that section.
If you know the protein domain family name or accession, ligand identifier or PDB identifier, the home page provides a quick and easier way of jumping into iPfam. The simplest way is to enter the term of interest in the ‘Jump To’ text field and click ‘Go’, as shown below:
As our protein family data is taken from Pfam, an accession will be of the for PFXXXXX, e.g. PF00018. The ligand identifiers are 3-character alphanumeric code assigns to each ligand by the PDB. A complete list of ligand identifier is the PDB can be found in the Chemical Component Dictionary. Occasionally the ligand or PDB identifier can clash with the name of a family, e.g. CBS, which corresponds to both a ligand and a family. Thus, if you are after the family, you may need to click on the ‘view a family entry’, otherwise click on the ‘view a ligand entry’.
The sequence and keyword searches link through to the main search options provided in the site, see below.