Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Networks

Protein Networks

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,...

Protein Networks

Protein Networks

Protein-protein Interfaces

Protein-protein Interfaces

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...

Protein-Protein Interfaces

Protein-Protein Interfaces

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

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...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

You might also read

Related Articles

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

Sort by

Same author

Exploring Confinement-Induced Self-Assembly of Anthracene in a Janus Inorganic Nanotube as a Route to Water-Dispersible Nanoscintillators.

Langmuir : the ACS journal of surfaces and colloids·2026

Same author

A Review on Efficient and Scalable Graph-Based Clustering Algorithms for Protein Complex Identification in PPI Networks.

Proteins·2025

Same author

Discerning Transuranic Sub-Concealments in Nuclear Waste Barrels Using γ-Ray Spectrometry: A Non-Invasive Assay Strategy To Combat the Threat of Nuclear Diversion.

ACS omega·2024

Same author

Comprehensive Evaluation of Bone Health Among Kidney Transplant Recipients - A Prospective, Single Center, Observational Cohort Study from India.

Journal of clinical densitometry : the official journal of the International Society for Clinical Densitometry·2024

Same author

Essential cancer protein identification using graph-based random walk with restart.

Computer methods in biomechanics and biomedical engineering·2024

Same author

Interrogating a Mixed Actinide Basket Using High-Resolution γ-Ray Spectrometry: A Nuclear Forensic Perspective on Possible Smuggling Scenarios.

Analytical chemistry·2024

Search research articles

Related Experiment Video

Updated: Dec 2, 2025

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

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

Published on: January 26, 2024

Protein complex prediction in interaction network based on network motif.

Sabyasachi Patra¹, Anjali Mohapatra¹

¹Bioinformatics Lab, Department of Computer Science, IIIT, Bhubaneswar, India.

Computational Biology and Chemistry

|November 5, 2020

Summary

This summary is machine-generated.

This study introduces a novel algorithm, CPNM, for predicting protein complexes from Protein-Protein Interaction (PPI) networks. CPNM leverages network motifs to improve accuracy and sensitivity in complex detection.

Keywords:

Biological network Feature matrix Feature normalization Neighborhood search Network motif Protein complex

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: March 3, 2015

Related Experiment Videos

Last Updated: Dec 2, 2025

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

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

Published on: January 26, 2024

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: March 3, 2015

Area of Science:

Computational Biology
Bioinformatics
Systems Biology

Background:

Protein-Protein Interaction (PPI) networks are vast, necessitating efficient computational methods for identifying protein complexes.
Existing algorithms struggle to balance accuracy and sensitivity in protein complex prediction.
Understanding protein complexes is crucial for deciphering cellular functions and disease mechanisms.

Purpose of the Study:

To propose a novel algorithm, Complex Prediction based on Network Motif (CPNM), for accurate and sensitive protein complex detection in PPI networks.
To enhance protein complex prediction by incorporating network motif roles and neighborhood search.
To evaluate CPNM's performance against established algorithms.

Main Methods:

Developed a novel algorithm (CPNM) utilizing network motifs to define protein feature vectors and weights.
Employed a neighborhood search technique to identify protein complexes based on protein roles and network density.
Evaluated CPNM using standard metrics: Precision, Recall, F-measure, Sensitivity, PPV, and Accuracy.

Main Results:

CPNM demonstrated superior performance compared to multiple existing algorithms (MCODE, DPClus, RNSC, COACH, ClusterONE, CMC, PROCODE).
The algorithm effectively identified protein complexes in both Saccharomyces cerevisiae and Homo sapiens PPI networks.
The findings highlight the efficacy of incorporating network motif information for improved complex prediction.

Conclusions:

CPNM offers a significant advancement in computational protein complex prediction.
The algorithm's approach, based on network motifs and neighborhood search, enhances accuracy and sensitivity.
CPNM provides a valuable tool for biological research requiring precise identification of protein complexes.