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

14.1K
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...
14.1K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.1K
4.1K
Protein Networks02:26

Protein Networks

4.2K
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,...
4.2K
Protein Networks02:26

Protein Networks

2.5K
2.5K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.7K
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...
2.7K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.0K
2.0K

You might also read

Related Articles

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

Sort by
Same author

Targeting of HSP27 and MMP-2/9 Crosstalk by High-Throughput Drug Repurposing Strategies Identifies Paroxetine as a Potential Candidate in Glioblastoma.

Journal of medicinal chemistry·2026
Same author

A transformer-based method for the cap analysis of gene expression and gene expression tag associated capping region prediction in RNA.

RNA biology·2026
Same author

Natural Compounds as Nephroprotective Agents: Therapeutic Potential Against Drug-Induced Kidney Injury.

Journal of biochemical and molecular toxicology·2025
Same author

Publisher Correction: Multimodal cell maps as a foundation for structural and functional genomics.

Nature·2025
Same author

Multimodal cell maps as a foundation for structural and functional genomics.

Nature·2025
Same author

rCGMM: A Coarse-Grained Force Field Embedding Elastic Network for Studying Small Noncoding RNA Dynamics.

The journal of physical chemistry. B·2025
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
Same journal

Generalizing the Gaussian Network Model: Spanning-Tree Thermodynamics Shows Entropy-Driven KRAS Activation.

Proteins·2026
See all related articles

Related Experiment Video

Updated: Nov 3, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.2K

A computational framework for modeling functional protein-protein interactions.

Abantika Pal1, Debnath Pal2, Pralay Mitra1

  • 1Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, India.

Proteins
|June 2, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces an automated computational framework to model protein-complex structures. It achieves an 83% success rate, aiding in understanding cellular mechanisms and identifying functional protein-protein interactions.

Keywords:
GO-based semantic similarityco-evolutionary informationprotein sequence homologyprotein-protein docking

More Related Videos

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

13.6K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.2K

Related Experiment Videos

Last Updated: Nov 3, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
06:50

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

2.2K
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
08:38

Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells

Published on: March 3, 2015

13.6K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

69.2K

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Understanding cellular mechanisms relies on mapping protein interactions and their assemblies within the interactome.
  • A significant gap exists between identified protein interactions and their known three-dimensional structures.
  • Computational modeling offers a viable solution to bridge this knowledge gap.

Purpose of the Study:

  • To develop an automated computational framework for modeling functionally related protein-complex structures.
  • To leverage Gene Ontology (GO)-based semantic similarity and co-evolutionary information for accurate modeling.
  • To provide a reliable tool for predicting protein-complex structures when experimental data is limited.

Main Methods:

  • Utilized Gene Ontology (GO)-based semantic similarity and co-evolutionary information of interaction sites.
  • Employed a framework accepting protein sequence and structure information as input.
  • Integrated rigid-body docking and template-based modeling, referencing Protein Data Bank (PDB) data.
  • Incorporated geometric and physicochemical features for re-ranking docking decoys.

Main Results:

  • Achieved an 83% success rate on a benchmark dataset.
  • Demonstrated high accuracy for Top1 models in template-based modeling.
  • Showcased effectiveness for Top10 models within the docking pipeline.
  • Validated the framework's capability in modeling protein-complex structures.

Conclusions:

  • The developed computational framework effectively models functionally related protein-complex structures.
  • This tool can reliably predict protein-protein interactions with higher confidence.
  • It addresses the challenge of uncharacterized protein complex structures in structural biology.