title: Predicting peroxidase subcellular location by hybridizing different descriptors of Chou' pseudo amino acid patterns.
abstract: Peroxidases as universal enzymes are essential for the regulation of reactive oxygen species levels and play major roles in both disease prevention and human pathologies. Automated prediction of functional protein localization is rarely reported and also is important for designing new drugs and drug targets. In this study, we first propose a support vector machine (SVM)-based method to predict peroxidase subcellular localization. Various Chou' pseudo amino acid descriptors and gene ontology (GO)-homology patterns were selected as input features to multiclass SVM. Prediction results showed that the smoothed PSSM encoding pattern performed better than the other approaches. The best overall prediction accuracy was 87.0% in a jackknife test using a PSSM profile of pattern with width=5. We also demonstrate that the present GO annotation is far from complete or deep enough for annotating proteins with a specific function.
authors.affiliation: The Key Laboratory of Mammalian Reproductive Biology and Biotechnology of the Ministry of Education, Inner Mongolia University, Hohhot 010021, China. Electronic address: yczuo@imu.edu.cn.
authors.forename: Yong-Chun
authors.initials: YC
authors.lastname: Zuo
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.affiliation: Center of Genomics and Computational Biology, College of Sciences, Hebei United University, Tangshan 063000, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China. Electronic address: yanglei_hmu@163.com.
authors.forename: Lei
authors.initials: L
authors.lastname: Yang
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China. Electronic address: eeguoliangfan@sina.com.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Fan
mesh_terms: D000596:Amino Acids / Q000737:chemistry / Q000378:metabolism; D002736:Chloroplasts / Q000201:enzymology / Q000378:metabolism; D003593:Cytoplasm / Q000201:enzymology / Q000378:metabolism; D016208:Databases, Factual; D004151:Dipeptides / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008928:Mitochondria / Q000201:enzymology / Q000378:metabolism; D009195:Peroxidase / Q000032:analysis*; D020675:Peroxisomes / Q000201:enzymology / Q000378:metabolism; D060388:Support Vector Machine
chemical_list: D000596:Amino Acids; D004151:Dipeptides; D009195:Peroxidase
keywords: Chou’ pseudo amino acid patterns; GO-homology annotation; Peroxidase proteins; Prediction performance