Jove
Visualize
Contact Us

Related Concept Videos

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 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
Protein Folding01:22

Protein Folding

117.7K
Overview
117.7K
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
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

17.7K
Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...
17.7K
Protein and Protein Structure02:15

Protein and Protein Structure

79.2K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
79.2K

You might also read

Related Articles

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

Sort by
Same author

Systemic Acquired Resistance signaling molecule N-hydroxypipecolic acid is involved in Age-Related Resistance in Arabidopsis thaliana.

Plant physiology·2026
Same author

Component puzzle protein-protein interaction prediction.

Briefings in bioinformatics·2025
Same author

Fast Variational Bayesian Inference for Correlated Survival Data: An Application to Invasive Mechanical Ventilation Duration Analysis.

Statistics in medicine·2025
Same author

Reply to: Insufficient evidence for natural selection associated with the Black Death.

Nature·2025
Same author

Mutational Patterns Observed in SARS-CoV-2 Genomes Sampled From Successive Epochs Delimited by Major Public Health Events in Ontario, Canada: Genomic Surveillance Study.

JMIR bioinformatics and biotechnology·2024
Same author

Scoring alignments by embedding vector similarity.

Briefings in bioinformatics·2024
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
Same journal

Correction: Pînzariu et al. Gut Microbiota and Short-Chain Fatty Acids: Key Factors in Pediatric Obesity and Therapeutic Targets. <i>Int. J. Mol. Sci.</i> 2025, <i>26</i>, 11503.

International journal of molecular sciences·2026
See all related articles
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 Experiment Video

Updated: Jun 16, 2025

Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

998

Explainability of Protein Deep Learning Models.

Zahra Fazel1, Camila P E de Souza2, G Brian Golding3

  • 1Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada.

International Journal of Molecular Sciences
|June 13, 2025
PubMed
Summary
This summary is machine-generated.

Explainable AI (XAI) methods reveal insights into protein embeddings, crucial for predicting protein interactions. Simple XAI approaches can be as effective as complex ones in uncovering essential biological information.

Keywords:
XAI methodsprotein embeddingsprotein interactions

More Related Videos

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
09:34

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

Published on: September 25, 2021

3.9K
Deep Neural Networks for Image-Based Dietary Assessment
13:19

Deep Neural Networks for Image-Based Dietary Assessment

Published on: March 13, 2021

9.0K

Related Experiment Videos

Last Updated: Jun 16, 2025

Author Spotlight: Advancing Alzheimer's Research &#8211; Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

998
A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data
09:34

A Virtual Machine Platform for Non-Computer Professionals for Using Deep Learning to Classify Biological Sequences of Metagenomic Data

Published on: September 25, 2021

3.9K
Deep Neural Networks for Image-Based Dietary Assessment
13:19

Deep Neural Networks for Image-Based Dietary Assessment

Published on: March 13, 2021

9.0K

Area of Science:

  • Proteomics
  • Computational Biology
  • Bioinformatics

Background:

  • Protein embeddings are vital for state-of-the-art solutions in proteomics, particularly for protein interaction prediction.
  • The black-box nature of these models necessitates transparency to understand underlying mechanisms.
  • Explainable AI (XAI) offers methods to investigate the inner workings of these complex models.

Purpose of the Study:

  • To investigate the interpretability of protein embedding models using XAI.
  • To evaluate the effectiveness of various XAI methods in uncovering essential protein properties and interactions.
  • To assess the quality of protein embeddings generated by different methods.

Main Methods:

  • Extensive testing of nine established XAI methods on 3.3 TB of data.
  • Application of XAI to protein interaction site prediction (Seq-InSite) and protein embedding generation (ProtBERT, ProtT5, Ankh).
  • Evaluation based on correlation with amino acid properties, interaction propensity, distant residue impact, and XAI infidelity scores.

Main Results:

  • Significant variation in the performance of different XAI methods was observed.
  • Simple XAI methods demonstrated comparable effectiveness to advanced ones in extracting key information.
  • Protein embeddings capture distinct properties, suggesting potential for enhanced embedding quality.

Conclusions:

  • XAI is crucial for understanding protein embeddings and their role in predicting protein interactions.
  • The choice of XAI method impacts the interpretability of protein embedding models.
  • There is considerable scope for improving protein embedding quality and the insights derived from them.