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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

Ligand Binding and Linkage

Ligand Binding and Linkage

Ligand Binding and Linkage

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 Equilibrium Binding Constant and Binding Strength

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:

Molecular Models

Molecular Models

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.

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Related Experiment Video

Updated: Mar 29, 2026

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

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

CHARMM-GUI Ligand Docker for Molecular Docking with Various Docking Programs.

Donghyuk Suh¹, Gyusik Kim², Wonpil Im¹

¹Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States.

Journal of Chemical Information and Modeling

|March 27, 2026

Summary

This summary is machine-generated.

CHARMM-GUI Ligand Docker simplifies molecular docking for drug discovery. This web tool integrates multiple docking engines and simulation workflows, enabling rapid and reproducible preparation of simulation-ready systems.

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Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Molecular docking is crucial for identifying ligand-receptor binding poses in drug discovery.
Preparing docking systems is a complex, time-consuming bottleneck.
Reproducibility in docking studies is often challenging.

Purpose of the Study:

To develop an automated, user-friendly platform for molecular docking and simulation system preparation.
To integrate multiple popular docking engines into a single framework.
To streamline the process of generating simulation-ready systems from docking results.

Main Methods:

Development of CHARMM-GUI Ligand Docker, a web-based tool.
Integration of AutoDock Vina, Smina, RxDock, and DiffDock.
Inclusion of PoseBuster for filtering docking poses.
Seamless transfer of poses to CHARMM-GUI High-Throughput Simulator.

Main Results:

CHARMM-GUI Ligand Docker provides a unified interface for docking calculations.
The platform simplifies receptor and ligand structure preparation and binding site definition.
Automated filtering and transfer to simulation workflows enhance reproducibility and efficiency.

Conclusions:

Ligand Docker significantly simplifies and accelerates the setup of molecular docking and simulation workflows.
The tool bridges the gap between docking and molecular dynamics simulations.
It serves as a valuable web resource for both expert and non-expert users in drug discovery.