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

3.7K
3.7K
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
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
Ligand Binding Sites02:40

Ligand Binding Sites

12.7K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.7K
Protein Organization01:24

Protein Organization

6.3K
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....
6.3K

You might also read

Related Articles

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

Sort by
Same author

Combined Administration of Cannabidiol and L-Theanine Improves Sleep-Related Outcomes in Caffeine-Induced Sleep Disturbances Mouse Model.

Biomolecules & therapeutics·2026
Same author

Low-Energy Light-Driven Excited-State Palladium Catalysis: Cross-Coupling of Pyridine <i>N</i>-Oxides with Unactivated Alkyl Bromides.

Organic letters·2026
Same author

Making invisible excited-state structures of pro-interleukin-18 visible by combining NMR and machine learning.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Retrospective study on the magnetic resonance imaging integration rate of acellular dermal matrix and complications after breast-conserving surgery plus radiotherapy.

World journal of surgical oncology·2026
Same author

A Real-World Efficacy and Safety of KEYNOTE-522 Regimen in Patients With Early Triple-Negative Breast Cancer.

Journal of breast cancer·2026
Same author

ASO Visual Abstract: Omitting Axillary Surgery for Patients with Ipsilateral Breast Tumor Recurrence After Breast-Conserving Surgery.

Annals of surgical oncology·2026

Related Experiment Video

Updated: Jun 9, 2025

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

1.7K

EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces.

Matthew McFee1,2, Jisun Kim2, Philip M Kim1,2,3

  • 1Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada.

Bioinformatics (Oxford, England)
|October 23, 2024
PubMed
Summary

We developed new scoring functions, EuDockScore and EuDockScore-Ab, using graph neural networks to improve protein-protein interaction predictions. A specialized model, EuDockScore-AFM, effectively reranks outputs from AlphaFold-Multimer for antibody-antigen complexes.

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K
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

13.3K

Related Experiment Videos

Last Updated: Jun 9, 2025

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

1.7K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.2K
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

13.3K

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Machine learning in protein science

Background:

  • Protein-protein interactions are crucial for biological processes, but predicting their structures computationally remains challenging.
  • Experimental structure determination is resource-intensive, necessitating accurate computational methods.
  • Scoring functions are vital for evaluating protein complex models generated by docking and deep learning.

Purpose of the Study:

  • To develop novel, high-performance scoring functions for protein-protein interactions.
  • To create specialized models for antibody-antigen complex assessment and reranking.
  • To leverage advanced Euclidean graph neural network architectures for improved accuracy.

Main Methods:

  • Utilized cutting-edge Euclidean graph neural network architectures.
  • Developed EuDockScore for general protein-protein interactions.
  • Created EuDockScore-Ab for antibody-antigen docking and EuDockScore-AFM for reranking AlphaFold-Multimer outputs.

Main Results:

  • Presented improved scoring functions (EuDockScore, EuDockScore-Ab) for assessing protein-protein interfaces.
  • Demonstrated the utility of EuDockScore-AFM in reranking large sets of antibody-antigen complex predictions from AlphaFold-Multimer.
  • Achieved enhanced accuracy in evaluating protein complex candidate structures.

Conclusions:

  • The developed EuDockScore models offer significant improvements in scoring protein-protein interactions.
  • EuDockScore-AFM provides an effective solution for filtering and prioritizing antibody-antigen complex predictions.
  • These advancements facilitate more accurate and efficient computational modeling of protein complexes.