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

You might also read

Related Articles

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

Sort by
Same author

Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension in <i>Xenopus</i>.

eLife·2026
Same author

<math></math> <i>vs</i> {Rmerg, Rmeas, Rpim, CC1/2} for Crystal Diffraction Data Quality Evaluation.

bioRxiv : the preprint server for biology·2024
Same author

Apoptotic signaling by TNFR1 is inhibited by the α2-6 sialylation, but not α2-3 sialylation, of the TNFR1 N-glycans.

The Journal of biological chemistry·2024
Same author

S. aureus Eap is a polyvalent inhibitor of neutrophil serine proteases.

The Journal of biological chemistry·2024
Same author

The Arf-GEF GBF1 undergoes multi-domain structural shifts to activate Arf at the Golgi.

Frontiers in cell and developmental biology·2023
Same author

Prickle and Ror modulate Dishevelled-Vangl interaction to regulate non-canonical Wnt signaling during convergent extension.

bioRxiv : the preprint server for biology·2023
Same journal

RETRACTED: Kim et al. The Angiogenesis Inhibitor ALS-L1023 from Lemon-Balm Leaves Attenuates High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease Through Regulating the Visceral Adipose-Tissue Function. <i>Int. J. Mol. Sci.</i> 2017, <i>18</i>, 846.

International journal of molecular sciences·2026
Same journal

Correction: Mahmud et al. Thymoquinone Attenuates NF-κβ Signalling Activation in Retinal Pigment Epithelium Cells Under AMD-Mimicking Conditions. <i>Int. J. Mol. Sci.</i> 2025, <i>26</i>, 11473.

International journal of molecular sciences·2026
Same journal

Correction: Borovikov et al. The Twisting and Untwisting of Actin and Tropomyosin Filaments Are Involved in the Molecular Mechanisms of Muscle Contraction, and Their Disruption Can Result in Muscle Disorders. <i>Int. J. Mol. Sci</i>. 2025, <i>26</i>, 6705.

International journal of molecular sciences·2026
Same journal

Correction: Molagoda et al. Flavonoid Glycosides from <i>Ziziphus jujuba</i> var. <i>inermis</i> (Bunge) Rehder Seeds Inhibit α-Melanocyte-Stimulating Hormone-Mediated Melanogenesis. <i>Int. J. Mol. Sci.</i> 2021, <i>22</i>, 7701.

International journal of molecular sciences·2026
Same journal

Correction: Guo et al. Integrated Transcriptomic and Metabolomic Analysis Reveals the Molecular Regulatory Mechanism of Flavonoid Biosynthesis in Maize Roots Under Lead Stress. <i>Int. J. Mol. Sci.</i> 2024, <i>25</i>, 6050.

International journal of molecular sciences·2026
Same journal

Correction: Chang et al. Improvement of Carbon Tetrachloride-Induced Acute Hepatic Failure by Transplantation of Induced Pluripotent Stem Cells Without Reprogramming Factor c-Myc. <i>Int. J. Mol. Sci.</i> 2012, <i>13</i>, 3598-3617.

International journal of molecular sciences·2026
See all related articles

Related Experiment Video

Updated: Aug 25, 2025

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

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.1K

AI-Based Protein Interaction Screening and Identification (AISID).

Zheng-Qing Fu1,2, Hansen L Sha3, Bingdong Sha3

  • 1SER-CAT, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA.

International Journal of Molecular Sciences
|October 14, 2022
PubMed
Summary
This summary is machine-generated.

This study introduces AISID, a method using AlphaFold-Multimer to predict protein interactions. AISID successfully identified correct pairings within the Tumor Necrosis Factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF), highlighting its potential for discovering novel protein bindings.

Keywords:
AISIDAlphaFoldcomputer-aided screeningproteins binding

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
Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
12:53

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

31.6K

Related Experiment Videos

Last Updated: Aug 25, 2025

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

Identifying Protein-protein Interaction Sites Using Peptide Arrays

Published on: November 18, 2014

18.1K
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
Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics
12:53

Identification of Protein Interaction Partners in Mammalian Cells Using SILAC-immunoprecipitation Quantitative Proteomics

Published on: July 6, 2014

31.6K

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biochemistry

Background:

  • AlphaFold-Multimer excels at protein structure prediction.
  • Identifying specific protein-protein interactions remains a challenge.
  • The Tumor Necrosis Factor superfamily (TNFSF) and TNF receptor superfamily (TNFRSF) play critical roles in cellular processes.

Purpose of the Study:

  • To develop and validate the AISID method for identifying specific protein interactions.
  • To extend the application of AlphaFold-Multimer beyond structure prediction.
  • To investigate TNFSF and TNFRSF interactions using the AISID method.

Main Methods:

  • Developed an optimized AISIDscore based on AlphaFold-Multimer.
  • Tested AISID on 18 human TNFSF members against 27 human TNFRSF members.
  • Ranked AISIDscores to identify correct protein pairings.

Main Results:

  • AISID correctly identified the highest-scoring interaction for 13 out of 24 known TNFRSF-TNFSF pairings.
  • 28 out of 33 correct TNFSF-TNFRSF pairings were ranked in the top five.
  • Identified novel interactions, including TNFSF10 (TRAIL) with decoy receptors, despite unknown structures.

Conclusions:

  • The AISID method, leveraging AlphaFold-Multimer, is a promising computational tool for screening specific protein-protein bindings.
  • AISID demonstrates broad applicability in protein biochemistry, expanding AlphaFold's utility.
  • This approach can accelerate the discovery of novel protein interactions.