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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...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2009
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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/. |
format | Text |
id | pubmed-2703882 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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