Objective To deduce all potential ligands undiscovered experimentally by searching all the proteins containing same C-termini

which can bind a certain PDZ domain. Methods We developed a JAVA program for searching short exact sequence matches at C-terminus. According to the known C-termini

which PDZ domains recognized experimentally

Swissprot database has been searched by this program for all potential ligands. Results Some PDZ domains may have more potential ligand proteins

which are undiscovered yet experimentally. These bioinformatic results also provide clues for studying functions of hypothetical proteins and PDZ domains’ protein interactions in many different organisms. Conclusion The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.