Prediction of DNA-binding residues from protein sequence information using random forests.
BACKGROUND
Protein-DNA interactions are involved in many biological processes essential for cellular function. To understand the molecular mechanism of protein-DNA recognition, it is necessary to identify the DNA-binding residues in DNA-binding proteins. However, structural data are available for only a few hundreds of protein-DNA complexes. With the rapid accumulation of sequence data, it becomes an important but challenging task to accurately predict DNA-binding residues directly from amino acid sequence data.


RESULTS
A new machine learning approach has been developed in this study for predicting DNA-binding residues from amino acid sequence data. The approach used both the labelled data instances collected from the available structures of protein-DNA complexes and the abundant unlabeled data found in protein sequence databases. The evolutionary information contained in the unlabeled sequence data was represented as position-specific scoring matrices (PSSMs) and several new descriptors. The sequence-derived features were then used to train random forests (RFs), which could handle a large number of input variables and avoid model overfitting. The use of evolutionary information was found to significantly improve classifier performance. The RF classifier was further evaluated using a separate test dataset, and the predicted DNA-binding residues were examined in the context of three-dimensional structures.


CONCLUSIONS
The results suggest that the RF-based approach gives rise to more accurate prediction of DNA-binding residues than previous studies. A new web server called BindN-RF http://bioinfo.ggc.org/bindn-rf/ has thus been developed to make the RF classifier accessible to the biological research community.
Wang
Liangjiang
L
Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA. liangjw@clemson.edu
Yang
Mary Qu
MQ
Yang
Jack Y
JY
D000465:Algorithms; D001185:Artificial Intelligence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D012372:ROC Curve; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D004268:DNA-Binding Proteins