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

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...

Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein Networks

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.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

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...

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...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:

You might also read

Related Articles

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

Sort by

Same author

Investigation and computational prediction of gating pore currents in Na<sub>V</sub>1.2 mutations across clinical phenotypes.

PNAS nexus·2026

Same author

A pore-facing glycan constrains GABA<sub>A</sub> receptor subunit stoichiometry and gating behavior.

Communications biology·2026

Same author

PUFA modulation of ASIC3 involves both specific and lipid solvent-like interactions.

bioRxiv : the preprint server for biology·2026

Same author

A Pore-Facing Glycan Determines GABAA Receptor Subunit Stoichiometry and Gating Behavior.

Research square·2025

Same author

The differential impacts of equivalent gating-charge mutations in voltage-gated sodium channels.

The Journal of general physiology·2025

Same author

Molecular Insights into Single-Chain Lipid Modulation of Acid-Sensing Ion Channel 3.

The journal of physical chemistry. B·2024

Search research articles

Related Experiment Video

Updated: May 26, 2025

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

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

Published on: February 23, 2024

Natural Language Processing Methods for the Study of Protein-Ligand Interactions.

James Michels¹, Ramya Bandarupalli², Amin Ahangar Akbari²

¹Department of Computer and Information Science, University of Mississippi, University, Mississippi 38677, United States.

Journal of Chemical Information and Modeling

|February 24, 2025

Summary

This summary is machine-generated.

Natural Language Processing (NLP) advances drug discovery by analyzing protein and ligand interactions. This review explores NLP methods for predicting these interactions, highlighting challenges and future directions.

More Related Videos

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Related Experiment Videos

Last Updated: May 26, 2025

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

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

Published on: February 23, 2024

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Analyzing Protein Architectures and Protein-Ligand Complexes by Integrative Structural Mass Spectrometry

Published on: October 15, 2018

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

Computational chemistry
Bioinformatics
Artificial intelligence

Background:

Natural Language Processing (NLP) is increasingly vital for studying protein and ligand binding, a key process in drug discovery.
Adapting NLP techniques to understand the 'language' of proteins and ligands can predict crucial interactions.

Purpose of the Study:

To review the application of NLP techniques in predicting protein-ligand interactions (PLIs).
To discuss advanced NLP methods and their role in decoding molecular interactions for drug development.

Main Methods:

Examination of NLP methods like Long Short-Term Memory (LSTM) networks, transformers, and attention mechanisms.
Leveraging diverse protein and ligand data types to identify interaction patterns using machine learning.

Main Results:

NLP models can analyze complex molecular data to predict potential protein-ligand interactions.
Identified challenges include data scarcity, model interpretability, and sampling biases.

Conclusions:

Improving data quality and model robustness is crucial for advancing machine learning in PLI prediction.
Collaboration and competition can accelerate progress in AI-driven drug discovery.