mUbiSiDa: a comprehensive database for protein ubiquitination sites in mammals

PLoS One. 2014 Jan 17;9(1):e85744. doi: 10.1371/journal.pone.0085744. eCollection 2014.

Abstract

Motivation: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Protein*
  • Humans
  • Information Storage and Retrieval
  • Mammals / metabolism*
  • Search Engine
  • Ubiquitination*

Grant support

The study was supported by grants from National Key Basic Research Program Grant (2011CB944304), National Natural Science Foundation of China (81222006, 61171191) and Natural Science Foundation of Jiangsu Province in China (BK2010500). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.