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...

Ligand Binding Sites

Ligand Binding Sites

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

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...

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...

You might also read

Related Articles

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

Sort by

Same author

hexABC seeking the physical code of DNA.

Nature communications·2026

Same author

The SLC15A4-LAMTOR1 interaction licenses endolysosomal TLR-mediated mTOR signaling and inflammatory cytokine production.

bioRxiv : the preprint server for biology·2026

Same author

Author Correction: Posttranslational modifications remodel proteome-wide ligandability.

Nature chemical biology·2026

Same author

Genetic and pharmacological inactivation of peptidoglycan remodeling increases antibiotic susceptibility of vancomycin-resistant Enterococcus faecium.

Nature communications·2026

Same author

Posttranslational modifications remodel proteome-wide ligandability.

Nature chemical biology·2026

Same author

How and Why Does Knowledge-Based Biased Docking Improve Molecular Docking Performance?

ChemMedChem·2026

Search research articles

Related Experiment Video

Updated: Nov 11, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Biased Docking for Protein-Ligand Pose Prediction.

Juan Pablo Arcon^1,2, Adrián G Turjanski³, Marcelo A Martí³

¹Departamento de Química Biológica e IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires, Argentina. juan.arcon@irbbarcelona.org.

Methods in Molecular Biology (Clifton, N.J.)

|March 24, 2021

Summary

This study introduces the AutoDock Bias protocol to improve protein-ligand docking accuracy. By incorporating target-specific interactions, this method enhances pose prediction for drug development.

Keywords:

AutoDock AutoDock Bias Biased docking Cosolvent Docking Guided docking Knowledge-based docking Mixed-solvents

More Related Videos

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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: Nov 11, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 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

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

Computational chemistry and molecular modeling.
Structural biology and drug discovery.

Background:

Protein-ligand interactions are fundamental to biological processes and drug development.
Molecular docking predicts protein-ligand complex structures but is system-dependent.
AutoDock4 is a popular but performance-variable docking tool.

Purpose of the Study:

To present the AutoDock Bias protocol for enhancing docking accuracy.
To demonstrate incorporating target-specific information into docking procedures.
To improve protein-ligand pose prediction and virtual screening.

Main Methods:

Application of the AutoDock Bias protocol using modified scoring functions.
Incorporation of target-specific interaction information (e.g., from crystal structures).
Utilizing biases derived from molecular dynamics simulations (e.g., hydrophobic interactions).

Main Results:

Demonstrated successful steering of docking towards desired ligand poses.
Showcased bias application using crystal structure-derived and simulation-derived interactions.
Evaluated performance in pose prediction and virtual screening campaigns.

Conclusions:

The AutoDock Bias protocol effectively overcomes limitations of standard docking methods.
Target-specific biases significantly improve the accuracy of protein-ligand complex prediction.
Biased docking offers a versatile strategy for drug discovery and other applications.