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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W325-30. doi: 10.1093/nar/gku383. Epub 2014 May 31.

GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.

Author information

  • 1State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
  • 2Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
  • 3Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China xueyu@hust.edu.cn.
  • 4State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China renjian.sysu@gmail.com.

Abstract

Small ubiquitin-like modifiers (SUMOs) regulate a variety of cellular processes through two distinct mechanisms, including covalent sumoylation and non-covalent SUMO interaction. The complexity of SUMO regulations has greatly hampered the large-scale identification of SUMO substrates or interaction partners on a proteome-wide level. In this work, we developed a new tool called GPS-SUMO for the prediction of both sumoylation sites and SUMO-interaction motifs (SIMs) in proteins. To obtain an accurate performance, a new generation group-based prediction system (GPS) algorithm integrated with Particle Swarm Optimization approach was applied. By critical evaluation and comparison, GPS-SUMO was demonstrated to be substantially superior against other existing tools and methods. With the help of GPS-SUMO, it is now possible to further investigate the relationship between sumoylation and SUMO interaction processes. A web service of GPS-SUMO was implemented in PHP+JavaScript and freely available at http://sumosp.biocuckoo.org.

PMID:
24880689
PMCID:
PMC4086084
DOI:
10.1093/nar/gku383
[PubMed - indexed for MEDLINE]
Free PMC Article
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