title: GPS-SUMO: a tool for the prediction of sumoylation sites and SUMO-interaction motifs.
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.
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yubin
authors.initials: Y
authors.lastname: Xie
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yueyuan
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Shuai
authors.initials: S
authors.lastname: Jiang
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Wenzhong
authors.initials: W
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Weiping
authors.initials: W
authors.lastname: Mu
authors.affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
authors.forename: Zexian
authors.initials: Z
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China xueyu@hust.edu.cn.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xue
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Sciences, School of Advanced Computing, Sun Yat-sen University, Guangzhou 510275, China renjian.sysu@gmail.com.
authors.forename: Jian
authors.initials: J
authors.lastname: Ren
mesh_terms: D000465:Algorithms; D020407:Internet; D010766:Phosphorylation; D054730:Protein Interaction Domains and Motifs; D020539:Sequence Analysis, Protein; D025841:Small Ubiquitin-Related Modifier Proteins / Q000378:metabolism*; D012984:Software; D058207:Sumoylation
chemical_list: D025841:Small Ubiquitin-Related Modifier Proteins