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

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
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.4K
3.4K
Protein Networks02:26

Protein Networks

3.6K
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,...
3.6K
Protein Folding01:22

Protein Folding

112.1K
Overview
112.1K
Protein Organization01:24

Protein Organization

7.2K
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....
7.2K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.1K
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...
2.1K

You might also read

Related Articles

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

Sort by
Same author

Rescuing the Function of Missense-Mutated Tumor Suppressor <i>VHL</i> using Stabilizing Small Molecules.

bioRxiv : the preprint server for biology·2026
Same author

Variation at the R181 residue of p53 confers loss of p53 DNA binding cooperativity with the retention of mitochondrial-associated apoptosis.

Molecular cancer research : MCR·2026
Same author

Immunotherapy-induced hypersensitivity reaction to red tattoo ink.

JAAD case reports·2026
Same author

Nanoemulsion is an effective antimicrobial for methicillin-resistant <i>Staphylococcus aureus</i> in infected swine skin burn wounds.

Microbiology spectrum·2024
Same author

Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless.

Orphanet journal of rare diseases·2024
Same author

PPIscreenML: Structure-based screening for protein-protein interactions using AlphaFold.

bioRxiv : the preprint server for biology·2024

Related Experiment Video

Updated: Apr 23, 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

70.1K

PPIscreenML is a method for structure-based screening of protein-protein interactions using AlphaFold.

Victoria Mischley1,2, Johannes Maier3, Jesse Chen3

  • 1Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, United States.

Elife
|April 21, 2026
PubMed
Summary

We developed PPIscreenML, a new machine learning tool that accurately predicts protein-protein interactions using AlphaFold2 models. This method reliably distinguishes true interactions from false positives, advancing protein network construction.

Keywords:
molecular biophysicsnoneprotein complexprotein interactionsstructural biologystructure prediction

More Related Videos

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

2.8K
Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

17.7K

Related Experiment Videos

Last Updated: Apr 23, 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

70.1K
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

2.8K
Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

17.7K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-protein interactions are fundamental to cellular functions.
  • Accurate protein complex modeling is now possible with tools like AlphaFold2 (AF2).
  • Distinguishing true interactions from decoys in AF2 models remains a challenge.

Purpose of the Study:

  • To develop and benchmark a method for inferring protein-protein interactions from AF2 models.
  • To create a classification model that distinguishes interacting pairs from non-interacting decoys.
  • To enable screening of candidate protein pairings for building interaction networks.

Main Methods:

  • Trained a classification model, PPIscreenML, using AF2 models of known interacting and decoy protein pairs.
  • Evaluated PPIscreenML performance against existing methods like pDockQ and iPTM.
  • Tested generalization on structurally conserved protein superfamilies, including the tumor necrosis factor superfamily (TNFSF).

Main Results:

  • PPIscreenML significantly outperforms pDockQ and iPTM in identifying true protein-protein interactions.
  • The model demonstrates high accuracy in predicting ligand/receptor interactions within the TNFSF.
  • Performance on unseen complexes indicates strong generalization capabilities.

Conclusions:

  • PPIscreenML provides a robust, benchmarked approach for identifying protein-protein interactions using structural models.
  • The tool is broadly applicable for discovering novel protein complexes predicted by AF2.
  • This advances the use of structural modeling for mapping cellular interaction networks.