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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...

Conserved Binding Sites

Conserved Binding Sites

Ligand Binding Sites

Ligand Binding Sites

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.
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...

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Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Ligand Binding and Linkage

Ligand Binding and Linkage

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: Feb 11, 2026

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

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

Published on: July 2, 2010

RBind: computational network method to predict RNA binding sites.

Kaili Wang¹, Yiren Jian², Huiwen Wang¹

¹Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan, China.

Bioinformatics (Oxford, England)

|May 3, 2018

Summary

This summary is machine-generated.

Predicting non-coding RNA binding sites is crucial for understanding their function. A new network approach, RBind, accurately identifies these sites on RNA molecules, overcoming limitations of existing methods.

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

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Published on: July 2, 2010

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Area of Science:

Molecular Biology
Bioinformatics
Computational Biology

Background:

Non-coding RNAs (ncRNAs) are vital for cellular functions through molecular interactions.
Determining RNA structures and binding sites is challenging due to RNA flexibility.
Existing experimental structures of RNA-ligand and RNA-protein complexes are limited, hindering functional analysis.

Purpose of the Study:

To develop a novel computational method for predicting non-coding RNA binding sites.
To improve the accuracy and reliability of RNA binding site prediction compared to current algorithms.

Main Methods:

A network-based approach named RBind was developed for RNA binding site prediction.
RBind was rigorously benchmarked using established RNA-ligand and RNA-protein datasets.

Main Results:

RBind demonstrated reliable accuracy in predicting RNA binding sites.
The method achieved an average accuracy of 0.82 for RNA-ligand interactions and 0.63 for RNA-protein interactions.

Conclusions:

The RBind network approach offers a significant advancement in predicting RNA binding sites.
Accurate binding site prediction is essential for elucidating the functional roles of non-coding RNAs.