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

被引：1

作者：

Qin, Wenyi ^{[1
,2
]}

Zhao, Guijun ^{[1
,3
,4
]}

Carson, Matthew ^{[2
]}

Jia, Caiyan ^{[5
,6
]}

Lu, Hui ^{[1
,2
]}

机构：

[1] Shanghai Jiao Tong Univ, Shanghai Childrens Hosp, Shanghai Inst Med Genet, Shanghai, Peoples R China

[2] Univ Illinois, Dept Bioengn, Chicago, IL USA

[3] Minist Hlth, Key Lab Mol Embryol, Shanghai 200040, Peoples R China

[4] Shanghai Key Lab Embryo & Reprod Engn, Shanghai 200040, Peoples R China

[5] Beijing Jiaotong Univ, Sch Comp & Informat Technol, Beijing, Peoples R China

[6] Beijing Jiaotong Univ, Beijing Key Lab Traff Data Anal, Beijing, Peoples R China

来源：

IET SYSTEMS BIOLOGY | 2016年 / 10卷 / 01期

基金：

中国国家自然科学基金;

关键词：

molecular biophysics; DNA; binding energy; knowledge-based three-body potential; transcription factor; binding site prediction; structure-based statistical potential; TFBS prediction; direct contact; amino acids; DNA bases; neighbouring base; two-body potential; binding energy prediction; binding mutation prediction; PROTEIN-DNA INTERACTIONS; ALL-ATOM; ENERGY FUNCTION;

D O I：

10.1049/iet-syb.2014.0066

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

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.

引用

页码：23 / 29

页数：7

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