Finding potential ligands for PDZ domains by tailfit, a JAVA program.

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.