Knowledge-based three-body potential for transcription factor binding site prediction

Wenyi Qin; Guijun Zhao; Matthew Carson; Caiyan Jia; Hui Lu

Knowledge-based three-body potential for transcription factor binding site prediction

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Author(s): Wenyi Qin ^{1, 2}^{1, 2} ; Guijun Zhao ^{1, 3}^{1, 3} ; Matthew Carson ²² ; Caiyan Jia ⁴⁴ ; Hui Lu ^{1, 2}^{1, 2}
- Affiliations: 1: Shanghai Institute of Medical Genetics, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, People's Republic of China ;
  2: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA ;
  3: Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, People's Republic of China ;
  4: School of Computer and Information Technology & Beijing Key Lab of Traffic Data Analysis, Beijing Jiaotong University, Beijing, People's Republic of China
Source: Volume 10, Issue 1, February 2016, p. 23 – 29
DOI: 10.1049/iet-syb.2014.0066 , Print ISSN 1751-8849, Online ISSN 1751-8857

Received 31/12/2014, Accepted 31/05/2015, Revised 15/05/2015, Published 01/02/2016

A structure-based statistical potential is developed for transcription factor binding site (TFBS) prediction. Besides the direct contact between amino acids from TFs and DNA bases, the authors also considered the influence of the neighbouring base. This three-body potential showed better discriminate powers than the two-body potential. They validate the performance of the potential in TFBS identification, binding energy prediction and binding mutation prediction.

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