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...

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...

You might also read

Related Articles

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

Sort by

Same author

Author Correction: Geographics and bacterial networks differently shape the acquired and latent global sewage resistomes.

Nature communications·2026

Same author

Survival prediction from neural parametrization of diffusive processes.

Physical review. E·2026

Same author

Toward Objective Wound Edge Classification in Clinical Practice.

Experimental dermatology·2026

Same author

Update of the MSKCC nomogram for metastatic progression and its role in active surveillance: the Italian TPCP cohort.

Frontiers in oncology·2026

Same author

Environmental Personal Exposure Clusters to Investigate Multiple Sclerosis and Amyotrophic Lateral Sclerosis Progression.

Studies in health technology and informatics·2026

Same author

A machine learning-derived cardiovascular risk score in people with HIV: the ML-ICONA score.

American journal of preventive cardiology·2026

Same journal

Transcriptomic insights into epigenetic and immunomodulatory roles of nuclear histone genes in bladder cancer: A bioinformatics approach.

Advances in protein chemistry and structural biology·2026

Same journal

Investigating the immune-modulatory association of miRNAs in HPV-associated HNSCC individuals: A bioinformatics approach.

Advances in protein chemistry and structural biology·2026

Same journal

VISTA as a Double-Edged immune checkpoint molecule in cancer and autoimmunity.

Advances in protein chemistry and structural biology·2026

Same journal

Aptamers as immunomodulatory therapeutic alternatives targeting neglected tropical diseases (NTDs).

Advances in protein chemistry and structural biology·2026

Same journal

Peptides and peptidomimetics as immunomodulator agents targeting neglected tropical diseases.

Advances in protein chemistry and structural biology·2026

Same journal

Transcriptomic profiling reveals immune pathway dysregulation and key interferon-responsive genes in Systemic Lupus Erythematosus.

Advances in protein chemistry and structural biology·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Oct 26, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Network-based strategies for protein characterization.

Alessandra Merlotti¹, Giulia Menichetti², Piero Fariselli³

¹Department of Physics and Astronomy, University of Bologna, Bologna, Italy.

Advances in Protein Chemistry and Structural Biology

|August 3, 2021

Summary

This summary is machine-generated.

This study explores using network spectral properties from protein contact maps to understand protein folding and structure. These methods help analyze protein folding states and reconstruct 3D protein structures.

Keywords:

Graph embedding Laplacian of a graph Protein folding Protein structure Shortest path distance matrix

More Related Videos

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Related Experiment Videos

Last Updated: Oct 26, 2025

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics

Published on: October 19, 2021

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions

Published on: December 1, 2020

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

Protein structure characterization is crucial for understanding protein functions, folding dynamics, thermal stability, and diseases like prion disease.
The Protein Contact Map (PCM) provides a network representation of protein structure.
Spectral properties of these networks offer potential for generating informative observables.

Purpose of the Study:

To provide an overview of using spectral properties of networks derived from PCMs for protein analysis.
To demonstrate the application of network approaches for discriminating protein folding states.
To showcase the utility of these methods for reconstructing protein 3D structures.

Main Methods:

Reconstruction of networks from Protein Contact Maps (PCMs).
Analysis of spectral properties of the reconstructed networks.
Application of two distinct network approaches to a protein dataset.

Main Results:

The spectral properties of protein contact map networks can generate informative observables.
The applied network approaches successfully discriminated between different protein folding states.
The methods showed potential for reconstructing the 3D structure of proteins.

Conclusions:

Network analysis of PCMs, particularly their spectral properties, offers a powerful approach for protein structure characterization.
These computational methods can aid in understanding protein folding and disease mechanisms.
The study highlights the versatility of network science in structural biology.