PredSulSite: prediction of protein tyrosine sulfation sites with multiple features and analysis.
Tyrosine sulfation is a ubiquitous posttranslational modification that regulates extracellular protein-protein interactions, intracellular protein transportation modulation, and protein proteolytic process. However, identifying tyrosine sulfation sites remains a challenge due to the lability of sulfation sequences. In this study, we developed a method called PredSulSite that incorporates protein secondary structure, physicochemical properties of amino acids, and residue sequence order information based on support vector machine to predict sulfotyrosine sites. Three types of encoding algorithms-secondary structure, grouped weight, and autocorrelation function-were applied to mine features from tyrosine sulfation proteins. The prediction model with multiple features achieved an accuracy of 92.89% in 10-fold cross-validation. Feature analysis showed that the coil structure, acidic amino acids, and residue interactions around the tyrosine sulfation sites all contributed to the sulfation site determination. The detailed feature analysis in this work can help us to understand the sulfation mechanism and provide guidance for the related experimental validation. PredSulSite is available as a community resource at http://www.bioinfo.ncu.edu.cn/inquiries_PredSulSite.aspx.
Department of Chemistry, Nanchang University, Nanchang 330031, People's Republic of China.
Shu-Yun
SY
Huang
Shao-Ping
SP
Shi
Jian-Ding
JD
Qiu
Xing-Yu
XY
Sun
Sheng-Bao
SB
Suo
Ru-Ping
RP
Liang
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019000:Phosphotyrosine / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D012372:ROC Curve; D014443:Tyrosine / Q000031:analogs & derivatives* / Q000378:metabolism
D011506:Proteins; D019000:Phosphotyrosine; C005662:tyrosine O-sulfate; D014443:Tyrosine