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

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
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
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
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
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

156
Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...
156
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K

You might also read

Related Articles

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

Sort by
Same author

Novel role of Wip1 in p53-mediated cell homeostasis under non-stress conditions.

Cell cycle (Georgetown, Tex.)·2011
Same author

Globular adiponectin protects human umbilical vein endothelial cells against apoptosis through adiponectin receptor 1/adenosine monophosphate-activated protein kinase pathway.

Chinese medical journal·2011
Same author

Single-side organically functionalized Anderson-type polyoxometalates.

Chemistry (Weinheim an der Bergstrasse, Germany)·2011
Same author

Buildup of amphiphilic molecular bola from organic-inorganic hybrid polyoxometalates and their vesicle-like supramolecular assembly.

Chemistry (Weinheim an der Bergstrasse, Germany)·2011
Same author

Galphas-biased beta2-adrenergic receptor signaling from restoring synchronous contraction in the failing heart.

Science translational medicine·2011
Same author

The epidemiological, clinical, and laboratory features of sporadic Creutzfeldt-Jakob disease patients in China: surveillance data from 2006 to 2010.

PloS one·2011

Related Experiment Video

Updated: Jun 19, 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

1.8K

[Advances in using artificial intelligence for predicting protein-ligand binding affinity].

Yinan Yun1,2,3, Shimeng Liu3, Qi Dai1

  • 1School of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, Zhejiang, China.

Sheng Wu Gong Cheng Xue Bao = Chinese Journal of Biotechnology
|July 24, 2024
PubMed
Summary

Artificial intelligence (AI) enhances protein-ligand binding affinity (PLBA) prediction due to its accuracy and speed. This review covers AI

Keywords:
artificial intelligencedrug developmentenzyme engineeringprotein-ligand binding affinity

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

2.5K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.6K

Related Experiment Videos

Last Updated: Jun 19, 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

1.8K
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

2.5K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.6K

Area of Science:

  • Biochemistry and computational biology.

Background:

  • Protein-ligand binding affinity (PLBA) is vital for biological processes, drug discovery, and enzyme engineering.
  • Accurate PLBA calculation provides insights into protein function and guides therapeutic target identification.

Purpose of the Study:

  • To offer a comprehensive overview of artificial intelligence (AI) applications in PLBA prediction.
  • To discuss AI's role, resources, applications, challenges, and future directions in this field.

Main Methods:

  • Review of current AI methodologies and algorithms applied to PLBA prediction.
  • Analysis of AI's feature extraction capabilities and predictive accuracy.

Main Results:

  • AI demonstrates robust performance in predicting PLBA, outperforming traditional methods.
  • AI offers rapid calculations essential for large-scale drug screening and analysis.

Conclusions:

  • AI is a powerful tool revolutionizing PLBA prediction and its applications in drug discovery.
  • Addressing current challenges in AI for PLBA will further enhance its utility and impact.