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

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-Protein Interfaces

Protein-Protein Interfaces

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...

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:

Protein-Drug Binding: Determination Methods

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

You might also read

Related Articles

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

Sort by

Same author

Simulation of cell-size systems at long timescales with flexible protein structures.

bioRxiv : the preprint server for biology·2026

Same author

Small-molecule binding and sensing with a designed protein family.

Nature communications·2026

Same author

Dockground: Expanding the Resource to Protein-DNA Complexes.

Journal of molecular biology·2025

Same author

Modeling protein-small molecule conformational ensembles with PLACER.

Proceedings of the National Academy of Sciences of the United States of America·2025

Same author

Modeling CAPRI Targets of Round 55 by Combining AlphaFold and Docking.

Proteins·2025

Same author

Atomic context-conditioned protein sequence design using LigandMPNN.

Nature methods·2025

Search research articles

Related Experiment Video

Updated: Apr 17, 2026

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

Protein models docking benchmark 2.

Ivan Anishchenko¹, Petras J Kundrotas, Alexander V Tuzikov

¹Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, 66047; United Institute of Informatics Problems, National Academy of Sciences, Minsk, 220012, Belarus.

|February 26, 2015

Summary

This summary is machine-generated.

This study updates a benchmark set of protein models to evaluate protein-protein docking accuracy. The enhanced set features more realistic models and complexes, improving the reliability of docking method assessments.

Keywords:

modeling of protein complexes protein interactions protein modeling protein recognition structure prediction

More Related Videos

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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Related Experiment Videos

Last Updated: Apr 17, 2026

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

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

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Area of Science:

Structural biology
Computational biology
Bioinformatics

Background:

Protein-protein interactions are crucial for understanding biological processes.
Experimentally determined protein structures are limited, necessitating computational modeling.
Accurate protein models are essential for reliable docking simulations.

Purpose of the Study:

To present a major update to a benchmark set of protein models for evaluating protein-protein docking.
To provide a statistically reliable dataset resembling real-world protein modeling scenarios.
To assess the highest achievable accuracy of predicted protein complexes using the benchmark.

Main Methods:

Generation of six models per interactor with varying C(α) RMSD (1-6 Å) to native structures.
Development of a new approach for generating models that mimic real-case scenarios.
Expansion of the benchmark set to 165 complexes for increased statistical power.

Main Results:

The updated benchmark set includes more realistic protein models and a larger number of complexes.
The new modeling approach better reflects actual protein structure prediction scenarios.
The benchmark allows for estimation of maximal accuracy for predicted protein complexes (e.g., using CAPRI criteria).

Conclusions:

The updated benchmark set provides a robust resource for assessing protein-protein docking methods.
The dataset enhances the reliability of evaluating docking accuracy against realistic protein models.
This resource aids in advancing computational approaches for structural biology research.