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 nonspecif...

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Bibliographic Details
Published in:Nucleic acids research 2009-07, Vol.37 (suppl-2), p.W396-W401
Main Authors: Chu, Wen-Yi, Huang, Yu-Feng, Huang, Chun-Chin, Cheng, Yi-Sheng, Huang, Chien-Kang, Oyang, Yen-Jen
Format: Article
Language:English
Subjects:
Base Sequence
Binding Sites
DNA - chemistry
DNA-Binding Proteins - chemistry
Internet
Sequence Analysis, Protein
Software
Transcription Factors - chemistry
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Summary: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/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp449