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

Protein-protein Interfaces02:04

Protein-protein Interfaces

15.1K
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...
15.1K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.6K
4.6K
Conserved Binding Sites01:49

Conserved Binding Sites

5.3K
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...
5.3K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

6.0K
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...
6.0K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.2K
2.2K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.1K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
3.1K

You might also read

Related Articles

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

Sort by
Same author

Estimation of protein melting temperatures using small-ladder replica exchange simulations.

The Journal of chemical physics·2026
Same author

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.

Journal of chemical information and modeling·2026
Same author

Comparison of Protein-Glycosaminoglycan Interactions in ff14sb/GLYCAM06j-1 and CHARMM36m Force Fields.

Journal of chemical information and modeling·2026
Same author

Protein-Protein Interaction Stabilizers from MD Simulation-Derived Pharmacophores.

Journal of chemical information and modeling·2026
Same author

The vacuolar tauopathy-associated mutation D395G confers redox sensitivity to p97/VCP.

bioRxiv : the preprint server for biology·2026
Same author

In Silico Analysis of Potential Stabilizer Binding Sites at Protein-RNA Interfaces.

Computational and structural biotechnology journal·2026
Same journal

BioMatics 1.0: A Wasserstein Distance Approach for Next-Generation Multiple Sequence Alignment.

Proteins·2026
Same journal

Engineered HSP90-MP65 Bivalent Fusion Antigen: A Novel Vaccine Candidate Against Invasive Candidiasis.

Proteins·2026
Same journal

Physics-Based Energy Functions for Computational Protein Design.

Proteins·2026
Same journal

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides.

Proteins·2026
Same journal

Stabilization of Bone Morphogenetic Protein-2 at Physiological pH: Contrasting Roles of CHAPS and Arginine in Aggregation Inhibition.

Proteins·2026
Same journal

Structural Insights Into the Function of Leishmania major Adenylosuccinate Lyase.

Proteins·2026
See all related articles

Related Experiment Video

Updated: Apr 20, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.6K

iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement.

Christina E M Schindler1, Sjoerd J de Vries, Martin Zacharias

  • 1Physik Department T38, Technische Universität München, 85748, Garching, Germany.

Proteins
|November 18, 2014
PubMed
Summary
This summary is machine-generated.

Computational docking struggles with protein flexibility. The new iATTRACT method refines protein-protein complexes by allowing full interface flexibility, significantly improving structural model accuracy and native contact prediction.

Keywords:
docking minimizationflexible interface refinementinduced fitprotein-protein complex formationprotein-protein docking

More Related Videos

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K
A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

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

Published on: April 3, 2026

236

Related Experiment Videos

Last Updated: Apr 20, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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

Published on: June 20, 2025

1.6K
Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors
10:33

Development of Inhibitors of Protein-protein Interactions through REPLACE: Application to the Design and Development Non-ATP Competitive CDK Inhibitors

Published on: October 26, 2015

11.9K
A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English
14:34

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

Published on: April 3, 2026

236

Area of Science:

  • Structural biology
  • Computational biophysics
  • Bioinformatics

Background:

  • Protein-protein interactions are crucial for cellular functions, but experimental structural data for complexes remain limited.
  • Computational protein-protein docking aids in predicting complex structures but is often hindered by the challenge of protein flexibility, particularly at the interface.

Purpose of the Study:

  • To develop and evaluate a novel computational docking refinement approach, iATTRACT, that addresses protein flexibility during the docking process.
  • To improve the accuracy and reliability of protein-protein complex structure prediction.

Main Methods:

  • Developed iATTRACT, a docking refinement method incorporating simultaneous full interface flexibility and rigid body optimizations.
  • Utilized an atomistic molecular mechanics force field for intermolecular interactions and a structure-based force field for intramolecular contributions.
  • Systematically evaluated iATTRACT on a large protein-protein docking benchmark using an enriched decoy set with significant initial deviations.

Main Results:

  • iATTRACT demonstrated substantial improvements in sampling and significant enhancements in scoring/discrimination of near-native docking solutions.
  • Complexes with initial interface deviations up to 5.5 Å were refined to achieve much better agreement with native structures.
  • Observed favorable increases in the fraction of native contacts, reaching up to 70%.

Conclusions:

  • The iATTRACT approach effectively handles protein flexibility during docking refinement, leading to more accurate structural models of protein-protein complexes.
  • This method offers a valuable tool for complementing experimental studies and advancing the field of structural bioinformatics.