title: The prediction of protein structural class using averaged chemical shifts.
abstract: Knowledge of protein structural class can provide important information about its folding patterns. Many approaches have been developed for the prediction of protein structural classes. However, the information used by these approaches is primarily based on amino acid sequences. In this study, a novel method is presented to predict protein structural classes by use of chemical shift (CS) information derived from nuclear magnetic resonance spectra. Firstly, 399 non-homologue (about 15% identity) proteins were constructed to investigate the distribution of averaged CS values of six nuclei ((13)CO, (13)Cα, (13)Cβ, (1)HN, (1)Hα and (15)N) in three protein structural classes. Subsequently, support vector machine was proposed to predict three protein structural classes by using averaged CS information of six nuclei. Overall accuracy of jackknife cross-validation achieves 87.0%. Finally, the feature selection technique is applied to exclude redundant information and find out an optimized feature set. Results show that the overall accuracy increased to 88.0% by using the averaged CSs of (13)CO, (1)Hα and (15)N. The proposed approach outperformed other state-of-the-art methods in terms of predictive accuracy in particular for low-similarity protein data. We expect that our proposed approach will be an excellent alternative to traditional methods for protein structural class prediction.
authors.affiliation: Key Laboratory for NeuroInformation of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China. hlin@uestc.edu.cn
authors.forename: Hao
authors.initials: H
authors.lastname: Lin
authors.forename: Chen
authors.initials: C
authors.lastname: Ding
authors.forename: Qiang
authors.initials: Q
authors.lastname: Song
authors.forename: Ping
authors.initials: P
authors.lastname: Yang
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.forename: Ke-Jun
authors.initials: KJ
authors.lastname: Deng
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D030562:Databases, Protein; D019906:Nuclear Magnetic Resonance, Biomolecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein; D060388:Support Vector Machine
chemical_list: D011506:Proteins