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

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...
Ligand Binding Sites02:40

Ligand Binding Sites

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

The Equilibrium Binding Constant and Binding Strength

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:
Conserved Binding Sites01:49

Conserved Binding Sites

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 analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

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 the...

You might also read

Related Articles

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

Sort by
Same author

GLP-1R and GIPR crosstalk modulates insulinotropic signaling pathways.

Cell chemical biology·2026
Same author

Candimine as a natural scaffold for targeting squalene synthetase in Trypanosoma cruzi: insights from computational studies.

Molecular diversity·2026
Same author

Molecular mechanisms of naturally encoded signaling bias at the complement anaphylatoxin receptors.

Molecular cell·2026
Same author

Distinctive Behavior and Selective Modulation of PPARγ by Pentacyclic Triterpenoid Pomolic Acid and Hederagenin from <i>Rosa canina</i>.

Journal of agricultural and food chemistry·2026
Same author

Structural mechanism for noncanonical GPCR signaling in the Hedgehog pathway.

Nature structural & molecular biology·2026
Same author

Rare variant in intracellular loop-2 alters the spatial distribution and transducer coupling selectivity of the ghrelin receptor.

Molecular pharmacology·2026

Related Experiment Video

Updated: Jul 2, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Assessing the ligand native-like pose using a quantum mechanical-derived hydropathic score for protein-ligand

Brian Medel-Lacruz1,2, William J Zamora3,4,5, Enric Herrero1

  • 1Pharmacelera, Parc Científic de Barcelona (PCB), Barcelona, Spain.

Npj Drug Discovery
|July 1, 2026
PubMed
Summary

Identifying the correct drug-protein binding pose is key for drug discovery. This study shows hydropathicity scoring, considering conformational stress, accurately predicts near-native poses with 90% accuracy.

More Related Videos

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Related Experiment Videos

Last Updated: Jul 2, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Computational chemistry
  • Structural biology
  • Drug discovery

Background:

  • Accurate prediction of ligand-protein binding poses is essential for drug development.
  • Identifying the near-native binding pose in docking simulations remains a significant challenge.

Purpose of the Study:

  • To evaluate the effectiveness of hydropathicity-based scoring functions in identifying near-native ligand-protein binding poses.
  • To assess the performance of 3D hydropathicity atomic descriptors in distinguishing bioactive from decoy poses.

Main Methods:

  • Utilized a benchmarking dataset of 1000 ligand-protein complexes.
  • Assessed 3D hydropathicity atomic descriptors derived from empirical and quantum mechanical models.
  • Incorporated the influence of conformational stress into the analysis.

Main Results:

  • Hydropathicity-based scoring functions demonstrated significant potential in identifying near-native poses.
  • Achieved a predictive accuracy of approximately 90% when considering conformational stress.
  • Highlighted the importance of nonpolar/polar chemical features for pose discrimination.

Conclusions:

  • Simple hydropathicity scoring, when accounting for conformational stress, can effectively predict near-native ligand-protein binding poses.
  • Understanding nonpolar and polar interactions is crucial for successful drug-target recognition and optimization.
  • This approach aids in guiding hit-to-lead optimization in drug discovery.