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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...

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...

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...

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:

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...

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Related Experiment Video

Updated: Jun 18, 2026

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English

Published on: April 3, 2026

Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK).

S Nehru Viji¹, P Arun Prasad, N Gautham

¹CAS in Crystallography and Biophysics, University of Madras, Chennai-600025, India.

Journal of Chemical Information and Modeling

|December 9, 2009

Summary

This study introduces an efficient computational method for predicting how flexible ligands bind to protein receptors. The technique effectively samples conformational and docking spaces, identifying optimal ligand conformations and binding modes with high accuracy.

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Last Updated: Jun 18, 2026

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

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

Published on: June 20, 2025

Area of Science:

Computational chemistry
Structural biology
Drug discovery

Background:

Predicting protein-ligand interactions is crucial for drug discovery.
Efficiently sampling ligand conformational and docking space is a major challenge.
Existing docking methods can be computationally expensive.

Purpose of the Study:

To develop and validate a computationally efficient docking technique.
To simultaneously identify low-energy ligand conformations and high-scoring docking modes.
To extend a previously developed method for peptide conformational searching.

Main Methods:

Utilizing mutually orthogonal Latin squares for efficient docking space sampling.
Applying a variant of the mean field technique for sample analysis and optimization.
Extending the method to simultaneously search ligand conformation and docking space.

Main Results:

The method successfully identified optimal ligand conformations and docking modes for small organic molecules.
Tested on 45 protein-ligand complexes with 2-19 rotatable torsions.
Performance was comparable to or better than AutoDock 4.0 at lower computational cost.

Conclusions:

The proposed docking method offers an efficient and accurate approach for predicting protein-ligand associations.
This technique can simultaneously optimize ligand conformation and docking pose.
The method shows promise for accelerating drug discovery and development pipelines.