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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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.
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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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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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Protein-protein Interfaces02:04

Protein-protein Interfaces

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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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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: Aug 20, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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RLBind: a deep learning method to predict RNA-ligand binding sites.

Kaili Wang1, Renyi Zhou1, Yifan Wu1

  • 1School of Computer Science and Engineering, Central South University, Changsha 410083, China.

Briefings in Bioinformatics
|November 18, 2022
PubMed
Summary
This summary is machine-generated.

Predicting RNA-small molecule binding sites is crucial for drug discovery. A new deep learning model, RLBind, accurately identifies these sites using sequence and structural properties, outperforming existing methods.

Keywords:
RNA–small molecule binding sites predictiondeep learningglobal informationlocal informationsequence-dependent propertiesstructure-dependent properties

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

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Related Experiment Videos

Last Updated: Aug 20, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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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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Area of Science:

  • Computational Biology
  • Drug Discovery
  • Molecular Biology

Background:

  • Identifying RNA-small molecule binding sites is vital for developing novel RNA-targeted therapeutics.
  • Current methods for predicting these binding sites are limited, presenting a significant challenge.
  • RNA molecules offer diverse structures and functions, making them promising drug targets.

Purpose of the Study:

  • To develop a novel computational model for accurate prediction of RNA-small molecule binding sites.
  • To improve the extraction of sequence-dependent and structure-dependent features for binding site prediction.
  • To provide a tool for binding site prediction even when experimental RNA tertiary structures are unavailable.

Main Methods:

  • A deep learning model named RLBind was developed.
  • RLBind utilizes both global RNA sequence information and local neighbor nucleotide context.
  • The model employs a convolutional neural network architecture, a first for this specific prediction task.

Main Results:

  • RLBind demonstrated superior performance compared to existing state-of-the-art methods.
  • The model effectively integrates global and local RNA features for enhanced predictive accuracy.
  • RLBind shows promise as a valuable tool in RNA-targeted drug discovery.

Conclusions:

  • Combining global and local RNA sequence information significantly improves binding site prediction accuracy.
  • RLBind represents a significant advancement in computational approaches for identifying RNA-small molecule interactions.
  • This work facilitates the development of new RNA-targeted therapeutics.