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 Experiment Videos

Codep: maximizing co-evolutionary interdependencies to discover interacting proteins.

Elisabeth R M Tillier1, Laurence Biro, Ginny Li

  • 1Cancer Genomics & Proteomics, Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada. e.tillier@utoronto.ca

Proteins
|April 25, 2006
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

BPabZIP, a new bZIP protein motif that promotes binding near, and displacement of, nucleosomes.

bioRxiv : the preprint server for biology·2026
Same author

STING-STAT3-SOX18 Axis Drives EndMT and Epigenetic Reprogramming in SAVI Lung Fibrosis.

bioRxiv : the preprint server for biology·2026
Same author

Plasma membrane accessible cholesterol is regulated by ACC1 and lipid droplets.

bioRxiv : the preprint server for biology·2025
Same author

Spatial Analysis of Hereditary Diffuse Gastric Cancer Reveals Indolent Phenotype of Signet Ring Cell Precursors.

Molecular cancer research : MCR·2025
Same author

Direct ionic stress sensing and mitigation by the transcription factor NFAT5.

Science advances·2025
Same author

New frontiers in the biosynthesis of psychoactive specialized metabolites.

Current opinion in plant biology·2024
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

This study introduces Codep, a novel method for identifying interacting protein partners by maximizing co-evolutionary signals. It predicts protein interactions by aligning evolutionary patterns in protein families, enhancing our understanding of molecular interactions.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Interacting proteins, like ligands and receptors, often exhibit similar evolutionary patterns.
  • Predicting protein interactions traditionally relies on comparing phylogenetic trees or evolutionary distance matrices.

Purpose of the Study:

  • To introduce Codep, a new computational method for identifying interacting protein partners.
  • To leverage co-evolutionary signals for more accurate prediction of protein-protein interactions.

Main Methods:

  • Codep maximizes co-evolutionary signals by optimizing the order of sequences in multiple sequence alignments of two protein families.
  • This optimization aligns substitution patterns and maximizes interdependencies between amino acid sites across alignments.

Related Experiment Videos

  • Phylogenetic congruency is achieved by maximizing shared evolutionary signals.

    • Main Results:

    • The method successfully predicts interacting protein partners by identifying corresponding sequences after alignment optimization.
    • Efficacy demonstrated through computer simulations and analyses of diverse protein families.
    • The Codep program is available for academic use.

    Conclusions:

    • Codep offers a novel and effective approach to predict protein-protein interactions by focusing on co-evolutionary signals.
    • The method enhances the identification of interacting partners across different protein families.
    • This tool aids in understanding molecular interactions and biological pathways.