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

Assembly of Signaling Complexes01:30

Assembly of Signaling Complexes

6.2K
Multiprotein signaling complexes are formed in a dynamic process involving protein-protein interactions at the cytoplasmic domain of transmembrane receptors or enzymatic and non-enzymatic proteins associated with the receptor. These complexes ensure the activation and propagation of intracellular signals that regulate cell functions.
Interaction domains in cell signaling
Interaction domains recognize exposed features of their binding partners containing post-translationally modified sequences,...
6.2K
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

14.5K
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:
14.5K
Ligand Binding Sites02:40

Ligand Binding Sites

14.4K
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...
14.4K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.2K
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...
14.2K

You might also read

Related Articles

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

Sort by
Same author

Consensus Recommendations for Management of Darier Disease: A Practical Approach.

Dermatology and therapy·2026
Same author

AbTune: layer-wise selective fine-tuning of protein language models for antibodies.

Briefings in bioinformatics·2026
Same author

Molecular insights into the dual-glycoprotein surface layer of the oral bacterium Tannerella serpentiformis.

Journal of molecular graphics & modelling·2026
Same author

TRIP8b<sub>nano</sub> peptide prevents cAMP binding to HCN2 channels alleviating pain-like behaviors in rats with neuropathic pain.

The Journal of physiology·2026
Same author

Selective IL-23 Inhibition in Conventional Treatment-Refractory Pyoderma Gangrenosum: A Multicenter, Retrospective Study.

International journal of dermatology·2026
Same author

Leveraging MrkA Display on Self-Assembling Protein Nanoparticles for Enhanced Immune Activation.

ACS applied materials & interfaces·2026

Related Experiment Video

Updated: Nov 15, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

611

Understanding Docking Complexes of Macromolecules Using HADDOCK: The Synergy between Experimental Data and

Andrea Saponaro1, Vincenzo Maione2,3, Alexandre M J J Bonvin4

  • 1Department of Biosciences, University of Milan, Milan, Italy.

Bio-Protocol
|March 4, 2021
PubMed
Summary

This study presents a protocol for modeling protein complexes using HADDOCK software, integrating computational analysis with experimental data. This approach refines structural models for accurate protein-peptide and protein-protein complex characterization.

Keywords:
Biomolecular interactionsHADDOCKHCN channelsITCIntegrative ModellingMacromolecular complexMolecular dockingNMRRational mutagenesisTRIP8b

More Related Videos

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

751
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

1.8K

Related Experiment Videos

Last Updated: Nov 15, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

611
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

751
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

1.8K

Area of Science:

  • Structural biology
  • Computational biology
  • Biochemistry

Background:

  • Accurate modeling of macromolecular complexes is crucial for understanding biological processes.
  • Experimental data integration enhances the reliability of computational modeling.
  • The HADDOCK software facilitates the integration of diverse experimental data for structural modeling.

Purpose of the Study:

  • To illustrate a protocol for modeling protein-peptide complexes.
  • To demonstrate the synergistic use of in silico analysis and experimental data.
  • To provide a method applicable to protein-protein complexes of any size.

Main Methods:

  • Utilizing HADDOCK software for integrative modeling.
  • Incorporating experimental data, including NMR Chemical Shift Perturbations and biochemical interaction data, as restraints.
  • Employing rational mutagenesis for model validation.

Main Results:

  • Generation of reliable structural models for protein-peptide complexes.
  • Selection of a bona fide complex structure based on experimental validation.
  • Demonstration of the protocol's applicability to protein-protein complexes.

Conclusions:

  • The described protocol effectively models protein-peptide complexes by integrating computational and experimental approaches.
  • HADDOCK is a versatile tool for structural modeling of macromolecular complexes.
  • The method allows for the validation and selection of accurate structural models.