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

12.6K
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...
12.6K
Protein Networks02:26

Protein Networks

4.1K
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,...
4.1K
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

2.6K
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...
2.6K

You might also read

Related Articles

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

Sort by
Same author

A lipoprotein partner for the <i>Escherichia coli</i> outer membrane protein TolC.

eLife·2026
Same author

gapTrick-structural characterization of protein-protein interactions using AlphaFold.

Bioinformatics (Oxford, England)·2025
Same author

Competition between binding partners of yeast Pex3 affects peroxisome biology.

The FEBS journal·2025
Same author

AlphaPulldown2-a general pipeline for high-throughput structural modeling.

Bioinformatics (Oxford, England)·2025
Same author

Using deep-learning predictions reveals a large number of register errors in PDB depositions.

IUCrJ·2024
Same author

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.

Nature methods·2024
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
Same journal

Informative Relational Learning for Adverse Reaction Prediction with Enhanced Generalization to Novel Drugs.

Bioinformatics (Oxford, England)·2026
Same journal

An interpretable deep learning framework uncovers features governing CRISPR-Cas9 genome-editing efficiency.

Bioinformatics (Oxford, England)·2026
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Aug 20, 2025

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions
07:03

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions

Published on: December 23, 2022

3.0K

AlphaPulldown-a python package for protein-protein interaction screens using AlphaFold-Multimer.

Dingquan Yu1,2, Grzegorz Chojnowski1, Maria Rosenthal3

  • 1European Molecular Biology Laboratory Hamburg, Hamburg 22607, Germany.

Bioinformatics (Oxford, England)
|November 22, 2022
PubMed
Summary
This summary is machine-generated.

AlphaPulldown is a new Python package that simplifies protein-protein interaction (PPI) screening and modeling of protein complexes using AlphaFold-Multimer. This tool enhances high-throughput analysis of protein structures and interactions.

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

2.0K
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

13.4K

Related Experiment Videos

Last Updated: Aug 20, 2025

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions
07:03

Pulldown Assay Coupled with Co-Expression in Bacteria Cells as a Time-Efficient Tool for Testing Challenging Protein-Protein Interactions

Published on: December 23, 2022

3.0K
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

2.0K
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

13.4K

Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • AlphaFold-Multimer has achieved high accuracy in protein complex structure prediction.
  • There is a growing need for tools to facilitate the discovery of protein-protein interactions (PPIs) using structure prediction models.

Purpose of the Study:

  • To present AlphaPulldown, a Python package designed to streamline PPI screening and high-throughput modeling of higher-order oligomers.
  • To provide a user-friendly interface for leveraging AlphaFold-Multimer in PPI discovery and structural analysis.

Main Methods:

  • Development of a Python package, AlphaPulldown, with a command-line interface.
  • Integration of AlphaFold-Multimer for protein complex and oligomer modeling.
  • Inclusion of confidence scores and a graphical analysis tool for results interpretation.

Main Results:

  • AlphaPulldown effectively streamlines the process of PPI screening.
  • The package enables high-throughput modeling of complex protein structures and oligomers.
  • Users benefit from a convenient interface and analytical tools for assessing model confidence.

Conclusions:

  • AlphaPulldown facilitates the discovery of protein-protein interactions and the structural modeling of protein complexes.
  • The package enhances the utility of AlphaFold-Multimer for large-scale biological studies.
  • AlphaPulldown offers a valuable resource for researchers in structural biology and bioinformatics.