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Plos One : a Structural-based Strategy for Recognition of Transcription Factor Binding Sites, Volume 7

By Srinivasan, Narayanaswamy

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Book Id: WPLBN0003933165
Format Type: PDF eBook :
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Reproduction Date: 2015

Title: Plos One : a Structural-based Strategy for Recognition of Transcription Factor Binding Sites, Volume 7  
Author: Srinivasan, Narayanaswamy
Volume: Volume 7
Language: English
Subject: Journals, Science, Medical Science
Collections: Periodicals: Journal and Magazine Collection (Contemporary)
Historic
Publication Date:
Publisher: Plos

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Srinivasan, N. (n.d.). Plos One : a Structural-based Strategy for Recognition of Transcription Factor Binding Sites, Volume 7. Retrieved from http://netlibrary.net/


Description
Description : Scanning through genomes for potential transcription factor binding sites (TFBSs) is becoming increasingly important in this post-genomic era. The position weight matrix (PWM) is the standard representation of TFBSs utilized when scanning through sequences for potential binding sites. However, many transcription factor (TF) motifs are short and highly degenerate, and methods utilizing PWMs to scan for sites are plagued by false positives. Furthermore, many important TFs do not have well-characterized PWMs, making identification of potential binding sites even more difficult. One approach to the identification of sites for these TFs has been to use the 3D structure of the TF to predict the DNA structure around the TF and then to generate a PWM from the predicted 3D complex structure. However, this approach is dependent on the similarity of the predicted structure to the native structure. We introduce here a novel approach to identify TFBSs utilizing structure information that can be applied to TFs without characterized PWMs, as long as a 3D complex structure (TF/DNA) exists. This approach utilizes an energy function that is uniquely trained on each structure. Our approach leads to increased prediction accuracy and robustness compared with those using a more general energy function. The software is freely available upon request.

 

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