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 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

3.8K
3.8K
Protein Folding01:22

Protein Folding

118.0K
Overview
118.0K
Protein Organization01:24

Protein Organization

6.5K
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....
6.5K
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

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

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

eLife·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 journal

A human-specific genetic modifier reconfigures large-scale cortical network dynamics underlying behavioral performance.

bioRxiv : the preprint server for biology·2026
Same journal

<i>Staphylococcus aureus</i> uses a eukaryotic-like uridyltransferase to make UDP-GlcNAc for cell wall synthesis.

bioRxiv : the preprint server for biology·2026
Same journal

Dynamic redistribution of eIF4F controls cap-dependent translation initiation.

bioRxiv : the preprint server for biology·2026
Same journal

When does additional information improve accuracy of RNA secondary structure prediction?

bioRxiv : the preprint server for biology·2026
Same journal

Normative brain-state trajectories reveal deviation from healthy aging in Alzheimer's disease.

bioRxiv : the preprint server for biology·2026
Same journal

Noradrenergic infraslow rhythm during sleep is the critical link between heart-rate dynamics and memory consolidation.

bioRxiv : the preprint server for biology·2026
See all related articles

Related Experiment Video

Updated: Jun 29, 2025

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

68.7K

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

Victoria Mischley1,2, Johannes Maier3, Jesse Chen3

  • 1Cancer Signaling & Microenvironment Program, Fox Chase Cancer Center, Philadelphia PA 19111.

Biorxiv : the Preprint Server for Biology
|April 1, 2024
PubMed
Summary
This summary is machine-generated.

We developed PPIscreenML, a machine learning model to identify true protein-protein interactions from structural models. PPIscreenML accurately distinguishes interacting pairs from decoys, outperforming existing methods.

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

1.8K
Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.0K

Related Experiment Videos

Last Updated: Jun 29, 2025

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

68.7K
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
Identifying Protein-protein Interaction Sites Using Peptide Arrays
07:44

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.0K

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are fundamental to cellular functions.
  • Advances in protein structure prediction, like AlphaFold2 (AF2), generate accurate models of protein complexes.
  • A key challenge is determining the biological relevance of predicted protein pairs and screening potential interactions for network construction.

Conclusions:

  • PPIscreenML provides a robust, benchmarked method for inferring protein-protein interactions from structural models.
  • The model is broadly applicable for discovering novel protein complexes using AF2-generated structural data.
  • This tool aids in building more accurate protein interaction networks by filtering reliable interactions.