mUbiSiDa: a comprehensive database for protein ubiquitination sites in mammals.
BACKGROUND
Protein ubiquitination is one of the important post-translational modifications by attaching ubiquitin to specific lysine (K) residues in target proteins, and plays important regulatory roles in many cell processes. Recent studies indicated that abnormal protein ubiquitination have been implicated in many diseases by degradation of many key regulatory proteins including tumor suppressor, oncoprotein, and cell cycle regulator. The detailed information of protein ubiquitination sites is useful for scientists to investigate the mechanism of many cell activities and related diseases.


RESULTS
In this study we established mUbiSida for mammalian Ubiquitination Site Database, which provides a scientific community with a comprehensive, freely and high-quality accessible resource of mammalian protein ubiquitination sites. In mUbiSida, we deposited about 35,494 experimentally validated ubiquitinated proteins with 110,976 ubiquitination sites from five species. The mUbiSiDa can also provide blast function to predict novel protein ubiquitination sites in other species by blast the query sequence in the deposit sequences in mUbiSiDa. The mUbiSiDa was designed to be a widely used tool for biologists and biomedical researchers with a user-friendly interface, and facilitate the further research of protein ubiquitination, biological networks and functional proteomics. The mUbiSiDa database is freely available at http://reprod.njmu.edu.cn/mUbiSiDa.
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
Tong
T
Chen
State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
Tao
T
Zhou
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
Bing
B
He
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
Haiyan
H
Yu
State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
Xuejiang
X
Guo
Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
Xiaofeng
X
Song
State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing, China.
Jiahao
J
Sha
D000818:Animals; D030562:Databases, Protein; D006801:Humans; D016247:Information Storage and Retrieval; D008322:Mammals / Q000378:metabolism*; D057386:Search Engine; D054875:Ubiquitination