Protein folds recognized by an intelligent predictor based-on evolutionary and structural information.
Protein fold recognition is an important and essential step in determining tertiary structure of a protein in biological science. In this study, a model termed NiRecor is developed for recognizing protein folds based on artificial neural networks incorporated in an adaptive heterogeneous particle swarm optimizer. The main contribution of NiRecor is that it is a data-driven and highly-performing predictor without manually tuning control parameters for different data sets. In biological science, since evolutionary- and structure-based information of amino acid sequences is greatly important in determination of tertiary structure of a protein, accordingly, in NiRecor we employ two different feature sets, which involve position specific scoring matrix and secondary structure prediction matrix, to predict the structural classes of protein folds. The experimental results demonstrate the proposed method is powerful in predicting protein folds with higher precisions by improvements of 1.1 ∼7.8 percentages on three benchmark datasets by comparing with several existing predictors.
Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing Ministry of Education of China, Shanghai, 200240, China.|James Franck Institute, the University of Chicago, Chicago, Illinois, 60637.
Ngaam J
NJ
Cheung
School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
Xue-Ming
XM
Ding
Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing Ministry of Education of China, Shanghai, 200240, China.
Hong-Bin
HB
Shen
D019295:Computational Biology; D019143:Evolution, Molecular; D016571:Neural Networks, Computer; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins
NiRecor; heterogeneous search; neural network; particle swarm optimization; protein fold recognition