Accurate prediction of enzyme subfamily class using an adaptive fuzzy k-nearest neighbor method.
Amphiphilic pseudo-amino acid composition (Am-Pse-AAC) with extra sequence-order information is a useful feature for representing enzymes. This study first utilizes the k-nearest neighbor (k-NN) rule to analyze the distribution of enzymes in the Am-Pse-AAC feature space. This analysis indicates the distributions of multiple classes of enzymes are highly overlapped. To cope with the overlap problem, this study proposes an efficient non-parametric classifier for predicting enzyme subfamily class using an adaptive fuzzy r-nearest neighbor (AFK-NN) method, where k and a fuzzy strength parameter m are adaptively specified. The fuzzy membership values of a query sample Q are dynamically determined according to the position of Q and its weighted distances to the k nearest neighbors. Using the same enzymes of the oxidoreductases family for comparisons, the prediction accuracy of AFK-NN is 76.6%, which is better than those of Support Vector Machine (73.6%), the decision tree method C5.0 (75.4%) and the existing covariant-discriminate algorithm (70.6%) using a jackknife test. To evaluate the generalization ability of AFK-NN, the datasets for all six families of entirely sequenced enzymes are established from the newly updated SWISS-PROT and ENZYME database. The accuracy of AFK-NN on the new large-scale dataset of oxidoreductases family is 83.3%, and the mean accuracy of the six families is 92.1%.
Huang
Wen-Lin
WL
Institute of Information Engineering and Computer Science, Feng Chia University, Taichung, Taiwan.
Chen
Hung-Ming
HM
Hwang
Shiow-Fen
SF
Ho
Shinn-Ying
SY
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D003198:Computer Simulation; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry*; D017143:Fuzzy Logic; D005822:Genetic Vectors; D015233:Models, Statistical; D008962:Models, Theoretical; D010088:Oxidoreductases / Q000235:genetics; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D049490:Systems Biology
D000596:Amino Acids; D004798:Enzymes; D010088:Oxidoreductases