title: NAPS: a residue-level nucleic acid-binding prediction server.
abstract: 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.
authors.affiliation: Department of Bioengineering/Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Carson
authors.forename: Robert
authors.initials: R
authors.lastname: Langlois
authors.forename: Hui
authors.initials: H
authors.lastname: Lu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry*; D020407:Internet; D016601:RNA-Binding Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D004268:DNA-Binding Proteins; D016601:RNA-Binding Proteins