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 Complexes with Interchangeable Parts01:57

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 to...
Protein Complexes with Interchangeable Parts01:57

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 to...
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Networks02:26

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 Networks02:26

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,...

You might also read

Related Articles

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

Sort by
Same author

A dihydrouracil CRBN ligand mitigates IMiD associated safety liabilities in heterobifunctional targeted protein degrader.

Nature communications·2026
Same author

Using the behaviour change wheel framework to develop a rule-based chatbot to support varenicline adherence for smoking cessation.

Digital health·2025
Same author

Testing the Acceptability and Feasibility of a Gender-Informed Smoking Cessation mHealth App for Women: Mixed Methods Approach.

JMIR human factors·2025
Same author

Autoimmune Connective Tissue Diseases: Systemic Lupus Erythematosus and Rheumatoid Arthritis.

Rheumatic diseases clinics of North America·2025
Same author

The Impact of ChatGPT Exposure on User Interactions With a Motivational Interviewing Chatbot: Quasi-Experimental Study.

JMIR formative research·2025
Same author

A Gender-Informed Smoking Cessation App for Women: Protocol for an Acceptability and Feasibility Study.

JMIR research protocols·2024
Same journal

Haplotype-aware long-read error correction.

Algorithms for molecular biology : AMB·2026
Same journal

Extension of partial atom-to-atom maps: uniqueness and algorithms.

Algorithms for molecular biology : AMB·2026
Same journal

Lossless pangenome indexing using tag arrays.

Algorithms for molecular biology : AMB·2026
Same journal

Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer.

Algorithms for molecular biology : AMB·2026
Same journal

Probing transcription factor subsets in gene regulatory networks.

Algorithms for molecular biology : AMB·2026
Same journal

Comparing the ability of embedding methods on metabolic hypergraphs for capturing taxonomy-based features.

Algorithms for molecular biology : AMB·2026
See all related articles

Related Experiment Video

Updated: Jun 1, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

A new, fast algorithm for detecting protein coevolution using maximum compatible cliques.

Alex Rodionov1, Alexandr Bezginov, Jonathan Rose

  • 1The Edward S, Rogers Sr, Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada. arod@eecg.toronto.edu.

Algorithms for Molecular Biology : AMB
|June 16, 2011
PubMed
Summary
This summary is machine-generated.

The MatrixMatchMaker algorithm (MMM) detects protein coevolution by analyzing phylogenetic trees. A new version, MMMvII, significantly speeds up this process, enabling more detailed coevolutionary analyses.

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

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

Related Experiment Videos

Last Updated: Jun 1, 2026

JUMPn: A Streamlined Application for Protein Co-Expression Clustering and Network Analysis in Proteomics
07:28

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

Published on: October 19, 2021

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

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

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • The MatrixMatchMaker (MMM) algorithm was developed to detect similarities between phylogenetic trees and infer protein coevolution.
  • MMM identifies common submatrices within phylogenetic distance matrices, offering advantages over prior coevolution detection methods.
  • The original MMM algorithm suffered from excessively long execution times, limiting its practical application.

Purpose of the Study:

  • To address the computational limitations of the original MatrixMatchMaker algorithm.
  • To develop a faster and more efficient method for detecting protein coevolution.
  • To enable more extensive and intricate coevolutionary analyses.

Main Methods:

  • The study reframes the maximum submatrix problem as a multiple maximum clique subproblem on a protein pair graph.
  • A novel algorithm and program implementation, MMMvII, was developed based on this new approach.
  • The performance of MMMvII was evaluated against the original MMM algorithm.

Main Results:

  • The MMMvII algorithm achieved a speedup of over 600 times compared to the original MMM.
  • MMMvII demonstrated comparable accuracy to the original MMM in detecting coevolution.
  • The computational problem was successfully reduced to a multiple maximum clique subproblem.

Conclusions:

  • MMMvII significantly enhances the efficiency of coevolution detection.
  • The improved speed allows for more comprehensive and complex analyses of protein coevolution.
  • MMMvII facilitates deeper insights into evolutionary relationships and protein function.