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.

Site Map

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.

Home page

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.

Questions or comments? Send a mail to [email protected]

Howard Hughes Medical Institute


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