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

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

Protein-Protein Interfaces

4.4K
4.4K
Protein Networks02:26

Protein Networks

4.4K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.4K
Protein Networks02:26

Protein Networks

2.7K
2.7K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.8K
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...
2.8K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
2.1K

You might also read

Related Articles

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

Sort by
Same author

Structural basis of βKNL2 centromeric targeting mechanism and its role in plant-specific kinetochore assembly.

Nucleic acids research·2026
Same author

Understanding chemical reactions through multimedia resolution data artistic educational tool (MRDAET).

Protein science : a publication of the Protein Society·2026
Same author

Condensin II mediates resistance to genotoxic stress and prevents mitotic defects in Arabidopsis.

Plant physiology·2026
Same author

The C-terminal SUMOylation-dependent regulation of αKNL2 governs its centromere targeting and interaction with CENH3.

Plant communications·2025
Same author

Risk of genitourinary late effects after radiotherapy for prostate cancer associated with early changes in bladder shape.

Physics and imaging in radiation oncology·2025
Same author

Embarrassingly Agile-Data Visualization Methodology in Emergency Responses.

IEEE computer graphics and applications·2025

Related Experiment Video

Updated: Jan 6, 2026

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

884

Visual Analysis of Protein-Protein Interaction Docking Models Using COZOID Tool.

Jan Byska1,2, Adam Jurcik2, Katarina Furmanova2

  • 1Department of Informatics, University of Bergen, Bergen, Norway.

Methods in Molecular Biology (Clifton, N.J.)
|October 5, 2019
PubMed
Summary

This study introduces COZOID, a novel tool for protein-protein interaction (PPI) modeling. It combines template-free docking with evolutionary conservation to select accurate protein complex models.

Keywords:
COZOID toolConservation rateContact residueContact zoneMultiple sequence alignmentProtein dockingProtein–protein interactionsVisual selection

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.6K
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

1.1K

Related Experiment Videos

Last Updated: Jan 6, 2026

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

884
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.6K
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

1.1K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions and are often conserved throughout evolution.
  • Evolutionary conservation provides insights into protein structure and interaction preservation.
  • Existing template-based methods leverage evolutionary information for tasks like protein structure modeling and docking.

Purpose of the Study:

  • To develop a novel approach for selecting accurate protein-protein interaction models.
  • To integrate template-free docking with evolutionary conservation analysis for improved model selection.
  • To introduce the COZOID tool for analyzing and selecting protein complex models based on structural similarity.

Main Methods:

  • Utilized a template-free docking method combined with conservation-based selection.
  • Developed the COZOID tool for analyzing contact zones and selecting amino acids for docking restraints.
  • Modeled and docked homologous proteins using the developed protocol.
  • Employed COZOID's analytical modes to identify docking models most similar to original complex structures.

Main Results:

  • Successfully integrated template-free docking with evolutionary conservation for model selection.
  • Demonstrated a step-by-step protocol for visual selection of docking models.
  • COZOID effectively analyzes contact zones and guides docking restraints.
  • Identified docking models exhibiting high similarity to original protein complex structures.

Conclusions:

  • The COZOID tool offers a robust method for selecting accurate protein complex models.
  • Combining docking with evolutionary conservation analysis enhances the reliability of PPI modeling.
  • This approach aids in understanding the structural and functional conservation of protein complexes.