Name
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/. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1093/nar/gkp449 | NUCLEIC ACIDS RESEARCH |
Keywords | Field | DocType |
nucleotides,transcription factors,gene regulation,internet,dna,binding sites,transcription factor,dna binding proteins | Gene,Binding site,Biology,Nucleobase,Sequence-specific DNA binding,DNA-binding protein,Regulation of gene expression,DNA,Genetics,Molecular biology,Transcription factor | Journal |
Volume | Issue | ISSN |
37 | SUPnan | 0305-1048 |
Citations | PageRank | References |
12 | 0.63 | 10 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Wenyi Chu | 1 | 15 | 1.50 |
| Yu-Feng Huang | 2 | 22 | 2.38 |
| Chun-Chin Huang | 3 | 12 | 0.63 |
| Yi-Sheng Cheng | 4 | 12 | 0.63 |
| Chien-Kang Huang | 5 | 150 | 11.52 |
| Yen-Jen Oyang | 6 | 423 | 48.82 |