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

4.0K
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,...
4.0K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.8K
3.8K
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
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
Ligand Binding Sites02:40

Ligand Binding Sites

12.8K
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...
12.8K

You might also read

Related Articles

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

Sort by
Same author

Genomic insights into end-use grain quality and nutritional traits of an ancient Indian dwarf wheat (Triticum sphaerococcum Percival) population using a multi-locus genome-wide association study.

Journal of the science of food and agriculture·2026
Same author

Stabilising high-spin, high-valent transition-metal-oxo species in cucurbit[5]uril: correlating structure, spin state, and reactivity.

Physical chemistry chemical physics : PCCP·2026
Same author

Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.

Journal of chemical information and modeling·2026
Same author

Converging neurotrophic-immune signaling in autism spectrum disorder: integrative roles of klotho, GDNF/GFRA-1, IGF-1 and GLP-1 pathways.

Metabolic brain disease·2026
Same author

Systematic discovery of motif-based interactions of the auxiliary domains of USP family deubiquitinases.

Nature communications·2026
Same author

Effects of expressing a maleness gene in Anopheles gambiae cells using baculovirus as a gene delivery tool.

Parasites & vectors·2026

Related Experiment Video

Updated: Jul 5, 2025

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

8.0K

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.

Chop Yan Lee1, Dalmira Hubrich1, Julia K Varga2

  • 1Institute of Molecular Biology (IMB) gGmbH, 55128, Mainz, Germany.

Molecular Systems Biology
|January 15, 2024
PubMed
Summary
This summary is machine-generated.

AlphaFold-Multimer shows promise for predicting protein structures, especially domain-motif interactions using specific protein fragmentation. This approach identified novel disease-related interfaces in neurodevelopmental disorders, offering new molecular insights.

Keywords:
AlphaFoldBenchmarkingExperimental ValidationLinear MotifsProtein Interaction Interface Prediction

More Related Videos

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
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

1.9K

Related Experiment Videos

Last Updated: Jul 5, 2025

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

8.0K
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
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

1.9K

Area of Science:

  • Structural Biology
  • Computational Biology
  • Genomics

Background:

  • Structural resolution of protein interactions is crucial for understanding biological mechanisms and disease variants.
  • Most protein interactions lack structural data due to limitations in current computational and experimental tools.
  • Short linear motif interactions within disordered protein regions are particularly challenging to resolve structurally.

Purpose of the Study:

  • To evaluate AlphaFold-Multimer's performance in predicting domain-motif interactions.
  • To develop and apply a protein fragmentation strategy for enhanced interface prediction.
  • To identify and experimentally validate novel protein interfaces involved in neurodevelopmental disorders.

Main Methods:

  • Utilized AlphaFold-Multimer for structure prediction of protein interactions.
  • Developed a protein fragmentation strategy optimized for domain-motif interfaces.
  • Applied the strategy to human proteins implicated in neurodevelopmental disorders.
  • Experimentally corroborated predicted interfaces using specific protein pairs.

Main Results:

  • AlphaFold-Multimer demonstrated high sensitivity but limited specificity for domain-motif interactions with small protein fragments.
  • Sensitivity decreased with longer protein fragments or full-length proteins.
  • The developed fragmentation strategy enabled confident prediction of novel, disease-associated interfaces.
  • Experimental validation confirmed several predicted interfaces, including FBXO23-STX1B and PEX3-PEX19.

Conclusions:

  • A tailored protein fragmentation strategy enhances AlphaFold-Multimer's utility for predicting domain-motif interfaces.
  • This approach successfully identified novel, potentially disease-related protein interfaces in neurodevelopmental disorders.
  • The study highlights AlphaFold-Multimer's potential while underscoring the need for further development in interface prediction.