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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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Autores principales: Chu, Wen-Yi, Huang, Yu-Feng, Huang, Chun-Chin, Cheng, Yi-Sheng, Huang, Chien-Kang, Oyang, Yen-Jen
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703882/
https://www.ncbi.nlm.nih.gov/pubmed/19483101
http://dx.doi.org/10.1093/nar/gkp449
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author Chu, Wen-Yi
Huang, Yu-Feng
Huang, Chun-Chin
Cheng, Yi-Sheng
Huang, Chien-Kang
Oyang, Yen-Jen
author_facet Chu, Wen-Yi
Huang, Yu-Feng
Huang, Chun-Chin
Cheng, Yi-Sheng
Huang, Chien-Kang
Oyang, Yen-Jen
author_sort Chu, Wen-Yi
collection PubMed
description 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/.
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spelling pubmed-27038822009-07-01 ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors Chu, Wen-Yi Huang, Yu-Feng Huang, Chun-Chin Cheng, Yi-Sheng Huang, Chien-Kang Oyang, Yen-Jen Nucleic Acids Res Articles 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/. Oxford University Press 2009-07-01 2009-05-29 /pmc/articles/PMC2703882/ /pubmed/19483101 http://dx.doi.org/10.1093/nar/gkp449 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Chu, Wen-Yi
Huang, Yu-Feng
Huang, Chun-Chin
Cheng, Yi-Sheng
Huang, Chien-Kang
Oyang, Yen-Jen
ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title_full ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title_fullStr ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title_full_unstemmed ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title_short ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
title_sort protedna: a sequence-based predictor of sequence-specific dna-binding residues in transcription factors
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703882/
https://www.ncbi.nlm.nih.gov/pubmed/19483101
http://dx.doi.org/10.1093/nar/gkp449
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