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.


CONCLUSIONS
The results may provide useful clues for discovering potential functions of hypothetical proteins and new functions of known proteins.
Huang
Hai-Ming
HM
Department of Pathophysiology, National Key Laboratory of Medical Molecular Biology, Proteomics Research Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005.
Zhang
Ling
L
Cui
Qing-Hua
QH
Jiang
Tian-Zi
TZ
Ma
Su-Can
SC
Gao
You-He
YH
D000595:Amino Acid Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D008024:Ligands; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
D008024:Ligands; D011506:Proteins