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

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Allosteric Transitions

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...

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

You might also read

Related Articles

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

Sort by

Same author

Development of Cathepsin B‑Activatable Cell-Penetrating Peptides for Tumor Targeting.

ACS pharmacology & translational science·2026

Same author

Glycosaminoglycan-functionalized hydrogels for sustained delivery of tissue inhibitor of metalloproteinase-3 mediating matrix metalloprotease inhibition and extracellular matrix stabilization.

Bioactive materials·2026

Same author

<i>In Silico</i> Analysis of Serum Albumin Binding by Bone-Regenerative Hyaluronan-Based Molecules.

Pharmaceutics·2025

Same author

Heparan sulfate fine-tuned interleukin-1 (IL-1) signaling inhibits insulin secretion of grafted pancreatic islets.

Science advances·2025

Same author

<i>De Novo</i>-Designed APC/C Inhibitors Provide a Rationale for Targeting RING-Type E3 Ubiquitin Ligases.

Journal of medicinal chemistry·2025

Same author

Engineering spacer specificity of the Cre/loxP system.

Nucleic acids research·2024

Search research articles

Related Experiment Video

Updated: Mar 30, 2026

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Published on: January 5, 2024

Exploring Multiple Binding Modes Using Confined Replica Exchange Molecular Dynamics.

Massimiliano Anselmi^1,2, M Teresa Pisabarro¹

¹Structural Bioinformatics, BIOTEC TU Dresden , Tatzberg 47-51, 01307 Dresden, Germany.

Journal of Chemical Theory and Computation

|November 18, 2015

Summary

This study introduces a novel molecular dynamics method to accurately predict ligand binding modes and free energies. The approach enhances accuracy for diverse protein-ligand systems, improving drug discovery predictions.

More Related Videos

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Related Experiment Videos

Last Updated: Mar 30, 2026

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Author Spotlight: Evaluation of Protein-Condensate Dynamics in Live Human Cells

Published on: January 5, 2024

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Method for Efficient Refolding and Purification of Chemoreceptor Ligand Binding Domain

Published on: December 12, 2017

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Molecular docking is widely used for predicting ligand-receptor interactions.
Existing methods often show poor correlation between docking scores and experimental binding affinities, especially for novel systems.

Purpose of the Study:

To develop an improved computational method for predicting binding modes and binding free energies.
To address limitations of current docking approaches in accuracy and applicability to diverse systems.

Main Methods:

Utilized replica exchange molecular dynamics (REMD).
Incorporated a receptor-shaped piecewise potential to confine ligand search space.
Tested methodology on various protein-ligand systems.

Main Results:

Successfully located ligands in experimentally known binding sites for all tested cases.
Accurately predicted binding free energies.
Demonstrated efficient conformational space exploration.

Conclusions:

The developed method accurately predicts binding modes and free energies.
Offers a significant advantage in speed and applicability over existing methods.
Provides valuable insights into binding poses and energetic properties for experimental binding states.