title: Knowledge-based three-body potential for transcription factor binding site prediction.
abstract: 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.
authors.affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
authors.forename: Wenyi
authors.initials: W
authors.lastname: Qin
authors.affiliation: Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai 200040, People's Republic of China.
authors.forename: Guijun
authors.initials: G
authors.lastname: Zhao
authors.affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Carson
authors.affiliation: School of Computer and Information Technology & Beijing Key Lab of Traffic Data Analysis, Beijing Jiaotong University, Beijing, People's Republic of China.
authors.forename: Caiyan
authors.initials: C
authors.lastname: Jia
authors.affiliation: Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA. huilu.bioinfo@gmail.com.
authors.forename: Hui
authors.initials: H
authors.lastname: Lu
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism; D051188:Knowledge Bases; D015233:Models, Statistical; D011487:Protein Conformation; D020539:Sequence Analysis, Protein; D013816:Thermodynamics; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D014157:Transcription Factors
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