Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Ligand Binding Sites

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 Sites

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...

Hydrogen Bonds

Hydrogen Bonds

A hydrogen bond is formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another polar molecule, such as water (H2O), hydrogen fluoride (HF), or ammonia (NH3). The huge electronegativity difference between the H atom (2.1) and the atom to which it is bonded (4.0 for an F atom, 3.5 for an O atom, or 3.0 for an N atom), combined with the very small size of an H atom...

Hydrogen Bonds

Hydrogen Bonds

Hydrogen bonds are weak attractions between atoms that have formed other chemical bonds. One of these atoms is electronegative, like oxygen, and has a partial negative charge. The other is a hydrogen atom that has bonded with another electronegative atom and has a partial positive charge.
Hydrogen Bonds Control the World!
Because hydrogen has very weak electronegativity when it binds with a strongly electronegative atom, such as oxygen or nitrogen, electrons in the bond are unequally shared.

Metal-Ligand Bonds

Metal-Ligand Bonds

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...

Molecular Orbital Theory II

Molecular Orbital Theory II

Molecular Orbital Energy Diagrams

You might also read

Related Articles

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

Sort by

Same author

Burden and trends of chronic kidney disease due to type 2 diabetes mellitus in China and G20 countries, 1990-2023: a comparative analysis.

Frontiers in endocrinology·2026

Same author

The GmCYCLOPS paralogs regulate soybean nodulation and exhibit signatures during domestication.

Plant science : an international journal of experimental plant biology·2026

Same author

Linker-Driven Sampling of PROTAC-Induced Ternary Complexes.

Journal of medicinal chemistry·2026

Same author

Misconceptions in Unbound Volume of Distribution and Their Implications for Pharmacokinetic Scaling and Drug Design.

ACS medicinal chemistry letters·2026

Same author

Dual-Site Coordination Regulated Crystallization for High-Performance MAPbBr<sub>3</sub> X-ray Detection.

ACS applied materials & interfaces·2026

Same author

Correction to "Unlocking the Carbon Mitigation Potential of Green Infrastructure: Evidence from China's Sponge City Program".

Environmental science & technology·2026

Same journal

Epidemiological characteristics of amebiasis in Japan from 2001 to 2022.

PloS one·2026

Same journal

Longitudinal associations of academic stress with eating related patterns, nutrition, somatic indicators, and depressive symptoms in university students: A study protocol.

PloS one·2026

Same journal

Pollution removal efficiency enhancement by agricultural biomass additions in constructed wetlands: A framework integrating meta-analysis with explainable machine learning.

PloS one·2026

Same journal

Insulation failure mapping on power transformer bushing using FRA and electrostatic simulation.

PloS one·2026

Same journal

Enhancing medical Q&A systems with multimodal knowledge graphs and dual-layer attention mechanisms.

PloS one·2026

Same journal

UAMP: Consistent video object segmentation with uncertainty-aware memory propagation.

PloS one·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 31, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Hydrogen bonding penalty upon ligand binding.

Hongtao Zhao¹, Danzhi Huang

¹Department of Biochemistry, University of Zurich, Zurich, Switzerland.

|June 24, 2011

Summary

This summary is machine-generated.

A new method quantifies hydrogen bonding penalty during ligand binding. This approach improves molecular docking accuracy and identifies novel drug scaffolds, as demonstrated with EphB4 inhibitors.

More Related Videos

Elucidation of the Material Basis of Yiqi Qingjie Formula Against IgA Nephropathy Using UHPLC-Q-Orbitrap HRMS Integrated with Network Pharmacology

Elucidation of the Material Basis of Yiqi Qingjie Formula Against IgA Nephropathy Using UHPLC-Q-Orbitrap HRMS Integrated with Network Pharmacology

Published on: May 19, 2026

Related Experiment Videos

Last Updated: May 31, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Elucidation of the Material Basis of Yiqi Qingjie Formula Against IgA Nephropathy Using UHPLC-Q-Orbitrap HRMS Integrated with Network Pharmacology

Elucidation of the Material Basis of Yiqi Qingjie Formula Against IgA Nephropathy Using UHPLC-Q-Orbitrap HRMS Integrated with Network Pharmacology

Published on: May 19, 2026

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Ligand binding to proteins involves complex energetic changes, including the disruption of water-mediated hydrogen bonds and the formation of new protein-ligand hydrogen bonds.
Accurately quantifying these hydrogen bonding energy changes is crucial for predicting binding affinity and pose.
Existing methods may not fully capture the energetic contribution of hydrogen bond rearrangements during binding.

Purpose of the Study:

To develop and validate a novel method for evaluating the hydrogen bonding penalty in ligand-protein binding.
To demonstrate the utility of this method in improving molecular docking and free energy calculations.
To apply the method in a high-throughput screening campaign for identifying novel EphB4 inhibitors.

Main Methods:

Development of a new computational method to calculate the hydrogen bonding penalty, representing the energetic cost of breaking existing and forming new hydrogen bonds.
Integration of the hydrogen bonding penalty into a free energy calculation model.
Application of the method to filter poses in molecular docking and in a high-throughput screening campaign for EphB4 inhibitors.

Main Results:

The new method accurately calculates the hydrogen bonding penalty, which can filter unrealistic docking poses.
The integrated free energy calculation model achieved low root mean square errors (0.7 kcal/mol training, 1.1 kcal/mol test).
Application in a high-throughput docking campaign for EphB4 inhibitors led to the discovery of three novel scaffolds among seven tested.

Conclusions:

The hydrogen bonding penalty is a significant factor in ligand-protein binding that can be effectively quantified.
The developed method enhances the accuracy of binding energy calculations and molecular docking.
This approach is a valuable tool for drug discovery, enabling the identification of novel inhibitors with potent binding affinities.