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

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

12.9K
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...
12.9K
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
The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

12.9K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.9K
Molecular Models02:00

Molecular Models

38.4K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.4K

You might also read

Related Articles

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

Sort by
Same author

The Influence of Pore Characteristics on the Mechanical Properties of 3D-Printed Concrete Based on the Phase-Field Method.

Materials (Basel, Switzerland)·2026
Same author

Integrating Charge Equilibration with Equivariant Machine-Learning Interatomic Potentials.

Journal of chemical theory and computation·2026
Same author

Multiscale Investigation of CO<sub>2</sub>/Oil Competitive Adsorption and Interfacial Evolution in Shale Reservoirs.

ACS omega·2026
Same author

Tumor cell-intrinsic NSUN2 deficiency reprograms macrophages to sensitize non-small cell lung cancer to EGFR inhibitors by reversing immune evasion.

Neoplasia (New York, N.Y.)·2026
Same author

Therapeutic target exploration of Shugan Jianpi formula in liver fibrosis: an integrated lncRNA-mRNA co-expression network analysis.

Molecular genetics and genomics : MGG·2026
Same author

Prevalence and Pathogen Profiles of Yak Diarrhea in Ganzi Tibetan Autonomous Prefecture, Sichuan Province, China.

Pathogens (Basel, Switzerland)·2026
Same journal

Gaining biological insights through supervised data visualization.

Nature computational science·2026
Same journal

The inequalities of GPU access.

Nature computational science·2026
Same journal

Social technologies need societal alignment.

Nature computational science·2026
Same journal

The Quantum Optimization Benchmarking Library.

Nature computational science·2026
Same journal

Setting benchmarks for practical quantum utility of combinatorial optimization.

Nature computational science·2026
Same journal

Evidence of scaling advantage on an NP-complete problem with enhanced quantum solvers.

Nature computational science·2026
See all related articles

Related Experiment Video

Updated: Jul 6, 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

1.9K

Predicting binding motifs of complex adsorbates using machine learning with a physics-inspired graph representation.

Wenbin Xu1,2, Karsten Reuter2, Mie Andersen3,4

  • 1Chair for Theoretical Chemistry and Catalysis Research Center, Technische Universität München, Garching, Germany.

Nature Computational Science
|January 4, 2024
PubMed
Summary
This summary is machine-generated.

Machine learning models predict adsorbate binding and enthalpies in catalysis. This data-efficient approach uses graph kernels and Gaussian processes, showing strong performance on transition metals and alloys, even for new elements.

More Related Videos

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

2.6K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K

Related Experiment Videos

Last Updated: Jul 6, 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

1.9K
Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
10:21

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA

Published on: February 23, 2024

2.6K
Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

3.2K

Area of Science:

  • Catalysis
  • Materials Science
  • Computational Chemistry

Background:

  • Computational screening in heterogeneous catalysis is crucial for discovering new materials and reactions.
  • First-principles calculations are computationally expensive, limiting exploration of complex materials and reaction mechanisms.
  • Machine learning offers a more efficient alternative for predicting catalytic properties.

Purpose of the Study:

  • To develop a data-efficient machine learning model for predicting adsorbate binding motifs and adsorption enthalpies.
  • To apply the model to transition metals and their alloys, including complex adsorbates.
  • To enable efficient exploration of materials spaces in catalysis research.

Main Methods:

  • Utilized a customized Wasserstein Weisfeiler-Lehman graph kernel for feature extraction.
  • Employed Gaussian process regression for predictive modeling.
  • Incorporated an ensemble uncertainty estimation approach for active learning.

Main Results:

  • The model accurately predicted binding motifs and adsorption enthalpies for elemental transition metals.
  • Demonstrated good predictive performance on a transition metal alloy, extending beyond the training set.
  • Showcased the ability to predict properties for an out-of-domain transition metal with minimal new data.

Conclusions:

  • The developed data-efficient machine learning model effectively predicts adsorbate binding and enthalpies in heterogeneous catalysis.
  • The approach is applicable to complex materials like alloys and can be extended to new elements.
  • The model shows promise for integration into active learning strategies to accelerate catalyst discovery.