Related Experiment Video
Updated: Jul 6, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
ZIFIBI: Prediction of DNA binding sites for zinc finger proteins
Soo Young Cho1, Myungguen Chung, Minyoung Park
1Division of Molecular and Life Sciences, Hanyang University, Sa 3 dong, Ansan, Kyunggodo 425-791, Republic of Korea.
Abstract:
The cis-regulatory region of target genes is key elements in the transcriptional regulation of gene expression. Many of these cis-regulatory regions have not been identified by either biological experiments or computational methods. Recently, a few additional C(2)H(2) zinc finger transcription factor binding sites have been discovered. The majority of the zinc finger binding sites, however, are still unknown. In this study, we used publically available data to evaluate possible interaction patterns between nucleotides and the amino acids of zinc finger domains. We calculated the most probable state path of three nucleotides sequences using a Hidden Markov Model (HMM). We used these computations to predict C(2)H(2) zinc finger transcription factor binding sites in cis-regulatory regions of their target genes (http://bioinfo.hanyang.ac.kr/ZIFIBI/frameset.php).
Related Concept Videos
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Single-Strand DNA Binding Proteins
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

