NAPS: a residue-level nucleic acid-binding prediction server

Nucleic acid-binding proteins are involved in a great number of cellular processes. Understanding the mechanisms underlying these proteins first requires the identification of specific residues involved in nucleic acid binding. Prediction of NA-binding residues can provide practical assistance in the functional annotation of NA-binding proteins. Predictions can also be used to expedite mutagenesis experiments, guiding researchers to the correct binding residues in these proteins. Here, we present a method for the identification of amino acid residues involved in DNA- and RNA-binding using sequence-based attributes. The method used in this work combines the C4.5 algorithm with bootstrap aggregation and cost-sensitive learning. Our DNA-binding model achieved 79.1% accuracy, while the RNA-binding model reached an accuracy of 73.2%. The NAPS web server is freely available at http://proteomics.bioengr.uic.edu/NAPS.