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-protein Interfaces02:04

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 polypeptide...
Protein-Protein Interfaces02:04

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 polypeptide...
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,...
Confidence Coefficient01:24

Confidence Coefficient

The confidence coefficient is also known as the confidence level or degree of confidence. It is the percent expression for the probability, 1-α, that the confidence interval contains the true population parameter assuming that the confidence interval is obtained after sufficient unbiased sampling; for example, if the CL = 90%, then in 90 out of 100 samples the interval estimate will enclose the true population parameter. Here α is the area under the curve, distributed equally under both the...
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Protein Organization01:24

Protein Organization

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.

You might also read

Related Articles

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

Sort by
Same author

High-resolution reconstruction of cell-type-specific transcriptional regulatory processes from bulk sequencing samples.

Nature biotechnology·2026
Same author

Scaled Multidimensional Assays of Variant Effect Identify Sequence-Function Relationships in Hypertrophic Cardiomyopathy.

Circulation·2026
Same author

Phosphatidylserine and RhoB connect PI4P and PA metabolism to maintain plasma membrane identity.

The Journal of cell biology·2026
Same author

Predictions of protein-protein interactions and co-complex models with deep learning.

Current opinion in chemical biology·2026
Same author

Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.

Cell·2026
Same author

Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles.

Cell·2026

Related Experiment Video

Updated: Jun 27, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

An experimentally derived confidence score for binary protein-protein interactions.

Pascal Braun1, Murat Tasan, Matija Dreze

  • 1Center for Cancer Systems Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA 02115, USA.

Nature Methods
|December 9, 2008
PubMed
Summary

Researchers developed a new toolkit of four high-throughput assays to experimentally assess protein-protein interactions. This method provides a confidence score for interactions, improving interactome network analysis in biomedical research.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Related Experiment Videos

Last Updated: Jun 27, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interactions (PPIs) are crucial for understanding cellular functions and disease mechanisms.
  • Current methods lack a systematic way to experimentally validate the quality of PPIs identified in large-scale mapping studies.
  • Assessing the reliability of PPI data is essential for building accurate interactome networks.

Purpose of the Study:

  • To develop a standardized, high-throughput method for assessing the confidence of individual protein-protein interactions.
  • To create a toolkit of complementary assays for robust experimental validation.
  • To enable systematic scoring of PPIs within large-scale interactome networks.

Main Methods:

  • Developed a toolkit comprising four complementary, high-throughput protein interaction assays.
  • Benchmarked assays against positive (known interacting proteins) and random (non-interacting protein pairs) reference sets.
  • Trained a logistic regression model to integrate assay outputs and calculate interaction confidence probabilities.

Main Results:

  • The developed toolkit enables the experimental assessment of protein interaction quality.
  • A logistic regression model effectively combines data from multiple assays to predict true biophysical interactions.
  • The approach allows for the assignment of confidence scores to individual PPIs.

Conclusions:

  • The novel toolkit provides a standardized and empirical method for confidence scoring of protein-protein interactions.
  • This approach facilitates the systematic evaluation of PPIs, enhancing the reliability of interactome networks.
  • The method is applicable to tens of thousands of protein interactions, advancing biomedical research.