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

12.9K
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
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
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
Complexometric Titration: Ligands00:43

Complexometric Titration: Ligands

961
Different monodentate and polydentate ligands are used as complexing agents in complexometric titration reactions. The formation of complexes by mono- and bidentate ligands involves two or more intermediate steps, limiting their use as complexing agents. In comparison, polydentate ligands can form complexes with metal ions in a single-step process, facilitating sharper end points. This means polydentate ligands, such as amino carboxylic acid derivatives, are most commonly employed in...
961
Metal-Ligand Bonds02:51

Metal-Ligand Bonds

20.8K
The hemoglobin in the blood, the chlorophyll in green plants, vitamin B-12, and the catalyst used in the manufacture of polyethylene all contain coordination compounds. Ions of the metals, especially the transition metals, are likely to form complexes.
In these complexes, transition metals form coordinate covalent bonds, a kind of Lewis acid-base interaction in which both of the electrons in the bond are contributed by a donor (Lewis base) to an electron acceptor (Lewis acid). The Lewis acid in...
20.8K
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

You might also read

Related Articles

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

Sort by
Same author

Unlocking hidden biomolecular conformational landscapes in diffusion models at inference time.

Advances in neural information processing systems·2026
Same author

Structural basis of opioid receptor activation by PCP and ketamine.

Nature structural & molecular biology·2026
Same author

Structural dynamics of kappa opioid receptor interactions with β-arrestin 1.

Nature communications·2026
Same author

Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.

Journal of chemical information and modeling·2026
Same author

Structural insights into coffee bitter taste perception by TAS2R43 receptor.

Nature structural & molecular biology·2026
Same author

Struct2Query: Structure-Guided Virtual Screening via Composite-Molecule ROCS Queries Derived from Protein Pocket Similarity.

Journal of chemical information and modeling·2026
Same journal

Poisoning the Genome: Targeted Backdoor Attacks on DNA Foundation Models.

ArXiv·2026
Same journal

Mechanistic mathematical model of the in vitro infection dynamics of Bunyamwera and Batai viruses including MOI-dependent shortening of the eclipse phase.

ArXiv·2026
Same journal

AI-Driven Lumped-Element Modeling of Human Respiratory System for Studying Voice Mechanics.

ArXiv·2026
Same journal

Beyond Algorithms: Conceptual Innovation in Medical Imaging AI.

ArXiv·2026
Same journal

Feynman Kac Reweighted Schrödinger Bridge Matching for Surface-Based Tau PET Harmonization.

ArXiv·2026
Same journal

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3.

ArXiv·2026
See all related articles

Related Experiment Video

Updated: Jul 8, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

175

Enhancing Ligand Pose Sampling for Molecular Docking.

Patricia Suriana1, Ron O Dror1

  • 1Department of Computer Science, Stanford University.

Arxiv
|December 11, 2023
PubMed
Summary
This summary is machine-generated.

New pose sampling methods, GLOW (auGmented sampLing with sOftened vdW potential) and IVES (IteratiVe Ensemble Sampling), improve molecular docking accuracy. These methods enhance the generation of candidate ligand poses for better scoring function training and virtual screening.

More Related Videos

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.4K
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

1.1K

Related Experiment Videos

Last Updated: Jul 8, 2025

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

175
Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps
09:30

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

1.4K
Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
10:29

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors

Published on: May 9, 2025

1.1K

Area of Science:

  • Computational chemistry
  • Structural biology
  • Machine learning

Background:

  • Deep learning significantly enhances molecular docking for binding pose prediction and virtual screening.
  • Accurate candidate pose generation is crucial for training scoring functions and performing molecular docking.
  • Current pose sampling protocols often fail to generate near-native poses, limiting scoring function accuracy.

Approach:

  • Introduced two novel pose sampling protocols: GLOW (auGmented sampLing with sOftened vdW potential) and IVES (IteratiVe Ensemble Sampling).
  • Benchmarked GLOW and IVES for their effectiveness in sampling accurate ligand binding poses.
  • Validated performance on both experimentally determined and AlphaFold-generated protein structures.

Key Points:

  • GLOW and IVES improve the likelihood of sampling accurate poses, particularly for flexible binding pockets.
  • The methods show effectiveness across diverse protein structures.
  • Generated and released large-scale cross-docking datasets for training and testing scoring functions.

Conclusions:

  • The developed pose sampling protocols address limitations in current molecular docking methods.
  • GLOW and IVES facilitate more accurate scoring function development and virtual screening.
  • Open-source implementation and datasets are provided to advance research in the field.