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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

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...

Ligand Binding and Linkage

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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.
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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...

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Related Experiment Video

Updated: Feb 12, 2026

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Screening Traditional Chinese Medicine Compounds for Inhibiting UCHL3 Activity Based on Molecular Docking and Deubiquitinating Enzyme Probe Technology

Published on: November 22, 2024

Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method.

Woong-Hee Shin¹, Daisuke Kihara^2,3

¹Department of Biological Science, Purdue University, West Lafayette, IN, USA.

Methods in Molecular Biology (Clifton, N.J.)

|March 30, 2018

Summary

This summary is machine-generated.

This study introduces PL-PatchSurfer2, a novel computational tool for drug discovery. It enhances virtual screening accuracy for protein targets, even without crystal structures, accelerating the identification of potential drug compounds.

Keywords:

3DZD Drug discovery Molecular surface Protein–ligand interaction Three-dimensional Zernike descriptor Virtual screening

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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
Drug discovery
Structural biology

Background:

Virtual screening is crucial in drug discovery for identifying potential drug candidates.
Traditional methods often require experimental validation, which is time-consuming and resource-intensive.
Accurate prediction of ligand-receptor interactions is key to efficient drug development.

Purpose of the Study:

To introduce PL-PatchSurfer2, a novel structure-based virtual screening program.
To improve the accuracy and applicability of virtual screening in drug discovery.
To enable virtual screening for protein targets lacking experimental structures.

Main Methods:

Utilizes molecular surface representation with 3D Zernike descriptors.
Employs a surface-patch description for enhanced tolerance to structural variations.
Applies the program to identify physicochemical complementarities between protein and ligand surfaces.

Main Results:

PL-PatchSurfer2 demonstrates higher accuracy compared to conventional virtual screening programs.
Achieves improved performance on both apo (unbound) and computationally modeled receptor structures.
Shows effectiveness even when experimental crystal structures are unavailable.

Conclusions:

PL-PatchSurfer2 offers a significant advancement in structure-based virtual screening.
The program facilitates drug discovery for a broader range of protein targets.
It provides a valuable tool for medicinal chemists, reducing experimental screening efforts.