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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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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...
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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Ligand Binding and Linkage00:49

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Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
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Related Experiment Video

Updated: May 1, 2026

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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A model-based approach to identify binding sites in CLIP-Seq data.

Tao Wang1, Beibei Chen2, MinSoo Kim2

  • 1Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

Plos One
|April 10, 2014
PubMed
Summary
This summary is machine-generated.

MiClip is a new computational method that accurately identifies protein-RNA binding sites from cross-linking immunoprecipitation sequencing (CLIP-Seq) data. This approach enhances the reliability of RNA-binding protein target identification in molecular biology research.

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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) is a powerful technique for genome-wide identification of protein-RNA interactions.
  • Existing methods for analyzing CLIP-Seq data can be limited in their accuracy and ability to prioritize binding sites for validation.

Purpose of the Study:

  • To develop and validate a novel model-based approach, MiClip, for identifying high-confidence protein-RNA binding sites from CLIP-Seq datasets.
  • To improve the signal-to-noise ratio and increase the number of validated binding targets compared to existing methods.

Main Methods:

  • Development of a model-based algorithm (MiClip) that assigns probability scores to potential protein-RNA binding sites.
  • Testing the MiClip algorithm on HITS-CLIP and PAR-CLIP datasets.
  • Comparison of MiClip performance against established ad hoc methods and other published approaches.

Main Results:

  • MiClip demonstrated significantly higher signal/noise ratios for miRNA seed motif enrichment in HITS-CLIP data (17-301% increase).
  • In PAR-CLIP data, MiClip identified approximately 50% more validated binding targets than existing methods.
  • MiClip provides a probability score to aid in prioritizing experimental validation.

Conclusions:

  • MiClip offers a robust and improved method for analyzing CLIP-Seq data to identify protein-RNA binding sites.
  • The MiClip algorithm enhances the accuracy and efficiency of RNA-binding protein target discovery.
  • Accessible R package and web-based software are available for MiClip application.