Structure-based prediction of transcription factor binding sites using a protein-DNA docking approach

2008 ◽  
Vol 72 (4) ◽  
pp. 1114-1124 ◽  
Author(s):  
Zhijie Liu ◽  
Jun-Tao Guo ◽  
Ting Li ◽  
Ying Xu
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Docking Approach ◽  
Dna Docking

scholarly journals Prediction of Transcription Factor Binding Sites of SP1 on Human Chromosome1

2021 ◽  
Vol 11 (11) ◽  
pp. 5123
Author(s):  
Maiada M. Mahmoud ◽  
Nahla A. Belal ◽  
Aliaa Youssif
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Messenger Rna ◽  
Area Under The Curve ◽  
Noisy Data ◽  
Transcription Factor Binding Sites ◽  
Classification Problem ◽  
Transcription Factor Binding ◽  
K Nearest Neighbors ◽  
Factor Binding

Transcription factors (TFs) are proteins that control the transcription of a gene from DNA to messenger RNA (mRNA). TFs bind to a specific DNA sequence called a binding site. Transcription factor binding sites have not yet been completely identified, and this is considered to be a challenge that could be approached computationally. This challenge is considered to be a classification problem in machine learning. In this paper, the prediction of transcription factor binding sites of SP1 on human chromosome1 is presented using different classification techniques, and a model using voting is proposed. The highest Area Under the Curve (AUC) achieved is 0.97 using K-Nearest Neighbors (KNN), and 0.95 using the proposed voting technique. However, the proposed voting technique is more efficient with noisy data. This study highlights the applicability of the voting technique for the prediction of binding sites, and highlights the outperformance of KNN on this type of data. The study also highlights the significance of using voting.

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