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 Networks02:26

Protein Networks

3.9K
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,...
3.9K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.5K
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...
12.5K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
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...
4.2K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.8K
3.8K
Protein Organization01:24

Protein Organization

6.4K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
6.4K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K

You might also read

Related Articles

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

Sort by
Same author

<i>SocialViruses</i>: integrating quantitative phage-bacteria and phage-phage interaction networks for rational cocktail design.

Bioinformatics advances·2025
Same author

Reference Vector-guided Evolutionary Algorithm for cluster analysis of single-cell transcriptomes.

Computer methods and programs in biomedicine·2025
Same author

Iterative Level-0: A new and fast algorithm to traverse mating networks calculating the inbreeding and relationship coefficients.

Computers in biology and medicine·2023
Same author

Automatic Update Summarization by a Multiobjective Number-One-Selection Genetic Approach.

IEEE transactions on cybernetics·2022
Same author

Theory and practice of natural computing: tenth edition.

Neural computing & applications·2022
Same author

PhageCocktail: An R package to design phage cocktails from experimental phage-bacteria infection networks.

Computer methods and programs in biomedicine·2022
Same journal

MMFVS-Net: A triple-symmetric cross-attention network for multimodal optical image fusion and high-accuracy virtual staining of breast cancer tissues.

Computer methods and programs in biomedicine·2026
Same journal

A novel Milstein-stochastic epidemiologically-informed neural network for approaching epidemic dynamics: Application to Mpox disease.

Computer methods and programs in biomedicine·2026
Same journal

Accounting for approximation errors using surrogate-based parameter estimation of cardiac mechanics digital twins.

Computer methods and programs in biomedicine·2026
Same journal

Facial iPPG heatmap patterns based on period-aware autoencoder show association with carotid atherosclerosis towards non-contact hemodynamic assessment.

Computer methods and programs in biomedicine·2026
Same journal

Explainable machine learning models predict liver fibrosis risk and outcome in the general population: Development and multi-cohort external validation.

Computer methods and programs in biomedicine·2026
Same journal

Evaluation of surrogate endpoints for survival outcomes using the surrogate package in R.

Computer methods and programs in biomedicine·2026
See all related articles

Related Experiment Video

Updated: Jun 28, 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

1.8K

A protein-protein interaction network aligner study in the multi-objective domain.

Manuel Menor-Flores1, Miguel A Vega-Rodríguez1

  • 1Escuela Politécnica, Universidad de Extremadura,(1) Campus Universitario s/n, 10003 Cáceres, Spain.

Computer Methods and Programs in Biomedicine
|April 24, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces multi-objective optimization for comparing protein-protein interaction (PPI) network alignments. SAlign, BEAMS, and SANA are recommended for high-quality alignments, with faster options available under time constraints.

Keywords:
Gene ontology consistencyMulti-objective optimizationNetwork alignmentProtein-protein interactionSymmetric substructure score

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

7.3K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K

Related Experiment Videos

Last Updated: Jun 28, 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

1.8K
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

7.3K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.0K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Protein-protein interaction (PPI) network alignment is crucial for disease diagnosis and prevention.
  • Aligner performance varies due to challenges in balancing topological and biological quality.
  • Multi-objective optimization offers a robust method for analyzing conflicting alignment qualities.

Purpose of the Study:

  • To comprehensively study protein-protein interaction (PPI) network aligners within a multi-objective optimization framework.
  • To analyze and compare the topological and biological qualities of different PPI network alignment methods.
  • To provide insights into aligner performance considering both quality and runtime.

Main Methods:

  • Utilized Pareto dominance methodologies to compare alignments from various PPI network aligners.
  • Generated Pareto front graphs to visualize alignment qualities across different scenarios.
  • Ranked aligners based on topological, biological, and combined alignment quality, as well as average runtime.

Main Results:

  • SAlign, BEAMS, SANA, and HubAlign produced the best overall alignments.
  • SANA, SAlign, and HubAlign excelled in topological quality.
  • BEAMS, TAME, and WAVE led in biological quality.
  • SAlign and PISwap are recommended for high-quality alignments under time constraints.

Conclusions:

  • SANA is recommended for topological quality, BEAMS for biological quality, and SAlign for combined quality.
  • SANA and BEAMS exhibit above-average runtimes.
  • For time-sensitive applications, SAlign and PISwap offer high-quality alignments efficiently.