Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.
BACKGROUND
In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical-chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class.


RESULTS
The results show that the RF model achieves 91.41% overall accuracy with Matthew's correlation coefficient of 0.70 and an area under the receiver operating characteristic curve (AUC) of 0.913. To our knowledge, the RF method using the hybrid feature is currently the computationally optimal approach for predicting DNA-binding sites in proteins from amino acid sequences without using three-dimensional (3D) structural information. We have demonstrated that the prediction results are useful for understanding protein-DNA interactions.


BACKGROUND
DBindR web server implementation is freely available at http://www.cbi.seu.edu.cn/DBindR/DBindR.htm.
Wu
Jiansheng
J
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
Liu
Hongde
H
Duan
Xueye
X
Ding
Yan
Y
Wu
Hongtao
H
Bai
Yunfei
Y
Sun
Xiao
X
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D030562:Databases, Protein; D008958:Models, Molecular; D011485:Protein Binding; D012372:ROC Curve
D000596:Amino Acids; D004268:DNA-Binding Proteins; D004247:DNA