PDZ domains and ligands in PDZBase can be queried using sequence motifs (Prosite format). The standard IUPAC one-letter codes for the amino acids are used. The symbol `x' is used for a position where any amino acid is accepted. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square brackets `[ ]'. For example: [ALT] stands for Ala or Leu or Thr. Each element in a pattern is separated from its neighbor by a `-'.

Example: R-[IP]-X-N-[YHS]-T.

This pattern is translated as:

Arg-[Ile or Pro]-any-Asn-[Tyr or His or Ser]-Thr

Motifs in PDZ-domains are searched for in the entire sequence of the domain. For ligands only the C-terminal residue is considered. So, the motif search S-X-V against the ligands returns only those ligands that have S-X-V as there C-terminal motif.