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

14.9K
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...
14.9K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.6K
4.6K
Protein Networks02:26

Protein Networks

4.6K
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,...
4.6K
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 Sites02:40

Ligand Binding Sites

15.6K
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...
15.6K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

3.0K
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...
3.0K

You might also read

Related Articles

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

Sort by
Same author

Chemical language models for natural product discovery.

Natural product reports·2026
Same author

COFFEE-PRESC: A Fast Prescreening Method Using Compound Retrieval by Pairwise Positional Relationship of Representative Fragments.

Journal of chemical information and modeling·2026
Same author

The impact of social and solitary activities on loneliness in older rural male adults: A path analysis study.

The Journal of rural health : official journal of the American Rural Health Association and the National Rural Health Care Association·2026
Same author

SpatialPPIv2: Enhancing protein-protein interaction prediction through graph neural networks with protein language models.

Computational and structural biotechnology journal·2025
Same author

Loneliness and social participation among older Japanese adults: The influence of gender on social participation.

PloS one·2025
Same author

Reaction-conditioned generative model for catalyst design and optimization with CatDRX.

Communications chemistry·2025

Related Experiment Video

Updated: Mar 12, 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

1.5K

Rigid-Docking Approaches to Explore Protein-Protein Interaction Space.

Yuri Matsuzaki1, Nobuyuki Uchikoga2, Masahito Ohue3

  • 1Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo, Japan. matsuzaki@acls.titech.ac.jp.

Advances in Biochemical Engineering/Biotechnology
|November 11, 2016
PubMed
Summary

Computational methods, including protein-protein rigid docking, predict direct protein-protein interactions. This approach aids in understanding interaction mechanisms and specificity by analyzing protein tertiary structures and binding poses.

Keywords:
Protein dockingProtein–protein interactionSupercomputing

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
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

1.3K

Related Experiment Videos

Last Updated: Mar 12, 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

1.5K
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
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

1.3K

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Protein-protein interactions are fundamental to cellular functions and regulatory systems.
  • Rapid accumulation of protein data necessitates advanced methods for network analysis.
  • Understanding protein interactions is crucial for deciphering cellular mechanisms.

Purpose of the Study:

  • To review computational prediction methods for pairwise direct protein-protein interactions.
  • To highlight the role of protein tertiary structure in predicting interactions.
  • To explain how docking-based approaches aid in understanding interaction mechanisms and specificity.

Main Methods:

  • Focus on computational prediction methods for protein-protein interactions.
  • Utilizing protein tertiary structure data for interaction prediction.
  • Employing protein-protein rigid docking as a key computational technique.

Main Results:

  • Docking-based approaches can suggest binding poses of interacting partners.
  • Analysis of docking results helps elucidate interaction mechanisms.
  • Comparing binders and non-binders reveals interaction specificity from structural perspectives.

Conclusions:

  • Computational methods, particularly rigid docking, are valuable tools for predicting protein-protein interactions.
  • Structural viewpoints derived from docking enhance understanding of interaction specificity.
  • These methods contribute to mapping protein-protein interaction networks.