Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Fast barcode calling based on <i>k</i>-mer distances.

PNAS nexus·2026

Same author

Evolutionary transcriptomics unveils rapid changes of gene expression patterns in flowering plants.

Cell·2026

Same author

The first causal inference analysis of the Catalan Arthroplasty Register shows a positive effect of antibiotic-loaded bone cement on knee prosthesis survival.

Journal of experimental orthopaedics·2025

Same author

<i>xcms</i> in Peak Form: Now Anchoring a Complete Metabolomics Data Preprocessing and Analysis Software Ecosystem.

Analytical chemistry·2025

Same author

Inferring binding specificities of human transcription factors with the wisdom of crowds.

bioRxiv : the preprint server for biology·2025

Same author

Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

Communications biology·2025

Search research articles

Related Experiment Video

Updated: Mar 21, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Detecting and correcting the binding-affinity bias in ChIP-seq data using inter-species information.

Martin Nettling¹, Hendrik Treutler², Jesus Cerquides³

¹Institute of Computer Science, Martin Luther University, Halle (Saale), Germany. martin.nettling@informatik.uni-halle.de.

|May 12, 2016

Summary

This summary is machine-generated.

This study introduces a new method to correct DNA binding motif prediction bias in ChIP-seq data by using cross-species information. This approach improves motif accuracy, offering a clearer view of transcriptional gene regulation.

Keywords:

Binding-affinity bias ChIP-seq Evolution Gene regulation Phylogenetic footprinting Transcription factor binding sites

More Related Videos

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

Related Experiment Videos

Last Updated: Mar 21, 2026

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

Published on: March 7, 2018

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

Area of Science:

Genomics
Molecular Biology
Bioinformatics

Background:

Transcriptional gene regulation relies on DNA binding motifs.
ChIP-seq is crucial for identifying DNA binding sites but introduces bias.
Traditional motif prediction methods are distorted by binding-affinity bias.

Purpose of the Study:

To develop a method for detecting and correcting binding-affinity bias in motif prediction.
To improve the accuracy of DNA binding motif identification.
To refine the understanding of transcriptional gene regulation.

Main Methods:

Utilized inter-species information to detect and correct bias.
Developed a phylogenetic footprinting model.
Compared bias in reference species ChIP-seq data with orthologous regions in related species.

Main Results:

The binding-affinity bias in ChIP-seq is stronger than indirect bias in related species.
The phylogenetic footprinting model successfully detects and corrects bias.
Corrected motifs are softer and more accurate than traditionally predicted motifs.

Conclusions:

Published motifs are artificially sharpened compared to native motifs.
Current understanding of transcriptional gene regulation may be inaccurate due to bias.
Incorporating inter-species information advances the study of gene regulation.