title: Predicting homo-oligomers and hetero-oligomers by pseudo-amino acid composition: an approach from discrete wavelet transformation.
abstract: Many proteins exist in vivo as oligomers with different quaternary structural attributes rather than as individual chains. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. With the dramatic increase in the number of protein sequences submitted to the public databank, it is important for both basic research and drug discovery research to acquire the knowledge about possible quaternary structural attributes of their interested proteins in a timely manner. A high-throughput method (DWT_SVM), fusing discrete wavelet transform (DWT) and support vector machine (SVM) classifier algorithm with various physicochemical features, has been developed to predict protein quaternary structure. The accuracy in distinguishing candidate proteins as homo-oligomer or hetero-oligomer using the dataset R(2720) was 85.95% and 85.49% respectively by jackknife, showing that DWT_SVM is guide promising in predicting protein quaternary structures. The online service is available at http://bioinfo.ncu.edu.cn/Services.aspx . Protein sequences in FASTA format can be directly fed to the system OligoPred. The processed results will be presented in a diagram that includes the information of feature extraction and the classification error rate.
authors.affiliation: Department of Chemistry, Nanchang University, Xue Fu road 999, Nanchang, Jiangxi, PR China. jdqiu@ncu.edu.cn
authors.forename: Jian-Ding
authors.initials: JD
authors.lastname: Qiu
authors.forename: Xing-Yu
authors.initials: XY
authors.lastname: Sun
authors.forename: Sheng-Bao
authors.initials: SB
authors.lastname: Suo
authors.forename: Shao-Ping
authors.initials: SP
authors.lastname: Shi
authors.forename: Shu-Yun
authors.initials: SY
authors.lastname: Huang
authors.forename: Ru-Ping
authors.initials: RP
authors.lastname: Liang
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D019295:Computational Biology / Q000379:methods; D020407:Internet; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D058067:Wavelet Analysis
chemical_list: D000596:Amino Acids; D011506:Proteins