ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.
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/.
Chu
Wen-Yi
WY
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, ROC.
Huang
Yu-Feng
YF
Huang
Chun-Chin
CC
Cheng
Yi-Sheng
YS
Huang
Chien-Kang
CK
Oyang
Yen-Jen
YJ
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*
D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA