title: Accurate prediction of protein structural classes by incorporating predicted secondary structure information into the general form of Chou's pseudo amino acid composition.
abstract: Extracting good representation from protein sequence is fundamental for protein structural classes prediction tasks. In this paper, we propose a novel and powerful method to predict protein structural classes based on the predicted secondary structure information. At the feature extraction stage, a 13-dimensional feature vector is extracted to characterize general contents and spatial arrangements of the secondary structural elements of a given protein sequence. Specially, four segment-level features are designed to elevate discriminative ability for proteins from the α/β and α+β classes. After the features are extracted, a multi-class non-linear support vector machine classifier is used to implement protein structural classes prediction. We report extensive experiments comparing the proposed method to the state-of-the-art in protein structural classes prediction on three widely used low-similarity benchmark datasets: FC699, 1189 and 640. Our method achieves competitive performance on prediction accuracies, especially for the overall prediction accuracies which have exceeded the best reported results on all of the three datasets.
authors: College of Mathematics and Information Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, PR China.
authors: Liang
authors: L
authors: Kong
authors: College of Marine Life Science, Ocean University of China, Yushan Road, Qingdao 266003, PR China. Electronic address: zhanglichaoouc@126.com.
authors: Lichao
authors: L
authors: Zhang
authors: College of Mathematics and Information Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, PR China.
authors: Jinfeng
authors: J
authors: Lv
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D000818:Animals; D030562:Databases, Protein; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D060388:Support Vector Machine
chemical_list: D000596:Amino Acids
keywords: Secondary structure; Sequence similarity; Support vector machine