title: ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.
abstract: This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites: http://protedna.csbb.ntu.edu.tw/, http://protedna.csie.ntu.edu.tw/, http://bio222.esoe.ntu.edu.tw/ProteDNA/.
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, ROC.
authors.forename: Wen-Yi
authors.initials: WY
authors.lastname: Chu
authors.forename: Yu-Feng
authors.initials: YF
authors.lastname: Huang
authors.forename: Chun-Chin
authors.initials: CC
authors.lastname: Huang
authors.forename: Yi-Sheng
authors.initials: YS
authors.lastname: Cheng
authors.forename: Chien-Kang
authors.initials: CK
authors.lastname: Huang
authors.forename: Yen-Jen
authors.initials: YJ
authors.lastname: Oyang
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D004247:DNA / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D020407:Internet; D020539:Sequence Analysis, Protein; D012984:Software; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA