Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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...
12.8K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
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...
4.8K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K

You might also read

Related Articles

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

Sort by
Same author

Integrating cytological images and spatial transcriptomics for cell segmentation with DISSECT.

Nature computational science·2026
Same author

Organic Chemistry as a Catalyst for AI Innovation: Challenges, Methods, and Emerging Paradigms.

Chemical reviews·2026
Same author

Optical fibre gripper for high-performance 3D micromanipulation.

Nature·2026
Same author

Efficacy and safety of FangJiHuangQi granule in patients with heart failure: a protocol of randomized, placebo-controlled trial.

Frontiers in cardiovascular medicine·2026
Same author

REGγ Links Inflammation to Fibrosis in Post-Necrotizing Enterocolitis Intestinal Strictures by Activating Transforming Growth Factor-β/Smad3 Signaling.

The American journal of pathology·2026
Same author

Hierarchical and Ultrametric Barriers in the Energy Landscape of Jammed Granular Matter.

Physical review letters·2026

Related Experiment Video

Updated: Jun 26, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

2.5K

MultiModRLBP: A Deep Learning Approach for Multi-Modal RNA-Small Molecule Ligand Binding Sites Prediction.

Junkai Wang, Lijun Quan, Zhi Jin

    IEEE Journal of Biomedical and Health Informatics
    |May 13, 2024
    PubMed
    Summary

    Predicting RNA-small molecule binding sites is crucial for RNA drug discovery. The novel MultiModRLBP method, using deep learning and multi-modal features, accurately identifies these sites, even with similar RNA sequences but different structures.

    More Related Videos

    Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
    11:34

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

    Published on: August 9, 2019

    6.6K
    Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
    10:52

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

    Published on: September 28, 2017

    8.1K

    Related Experiment Videos

    Last Updated: Jun 26, 2025

    Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
    10:21

    Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

    Published on: February 23, 2024

    2.5K
    Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
    11:34

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

    Published on: August 9, 2019

    6.6K
    Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
    10:52

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

    Published on: September 28, 2017

    8.1K

    Area of Science:

    • Computational Biology
    • Drug Discovery
    • Structural Bioinformatics

    Background:

    • Predicting RNA-small molecule interactions is key for developing RNA-targeted drugs.
    • Identifying specific binding sites on RNA is a complex challenge due to RNA's structural versatility.

    Purpose of the Study:

    • To develop an accurate method for predicting RNA-small molecule binding sites.
    • To enhance the understanding of RNA-ligand interactions for drug development.

    Main Methods:

    • Proposed the Multi-modal Relational Learning for RNA Binding Prediction (MultiModRLBP) method.
    • Integrated multi-modal features: 3D structural properties, RNA relational graphs, and semantic information.
    • Utilized deep learning algorithms on an expanded dataset including RNA complexes with sequence similarity but structural variations.

    Main Results:

    • MultiModRLBP outperforms state-of-the-art methods on classic test sets.
    • Achieved high accuracy in predicting binding sites for non-metal ions and distributed binding instances.
    • Demonstrated capability in distinguishing binding characteristics of structurally diverse RNAs with sequence similarity.

    Conclusions:

    • MultiModRLBP is a promising tool for RNA drug target identification, especially when RNA structure is perturbed or unavailable.
    • The method aids in reducing drug development costs by improving prediction accuracy.
    • Advances in predicting RNA-small molecule binding sites pave the way for novel therapeutics.