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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

Conserved Binding Sites

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...

Conserved Binding Sites

Conserved Binding Sites

Molecular Chaperones and Protein Folding

Molecular Chaperones and Protein Folding

The native conformation of a protein is formed by interactions between the side chains of its constituent amino acids. When the amino acids cannot form these interactions, the protein cannot fold by itself and needs chaperones. Notably, chaperones do not relay any additional information required for the folding of polypeptides; the native conformation of a protein is determined solely by its amino acid sequence. Chaperones catalyze protein folding without being a part of the folded protein.
The...

Factors Affecting Protein-Drug Binding: Drug Interactions

Factors Affecting Protein-Drug Binding: Drug Interactions

Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...

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Related Experiment Video

Updated: Feb 5, 2026

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Published on: July 15, 2019

Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites.

Wei Xiao^1,2, Disha Wang³, Zihao Shen²

¹School of Information Science and Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China. xiaowei1012163@163.com.

Molecules (Basel, Switzerland)

|September 14, 2018

Summary

This study introduces a novel multi-body docking program that accurately models protein-ligand interactions by including key water molecules. This approach enhances docking accuracy and screening efficiency compared to traditional methods.

Keywords:

multi-body docking multi-objective optimization optimization variables water molecules

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Last Updated: Feb 5, 2026

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

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Published on: July 15, 2019

Identifying Protein-protein Interaction Sites Using Peptide Arrays

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Published on: November 18, 2014

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:

Traditional molecular docking methods often neglect the crucial role of water molecules in protein-ligand interactions.
Ignoring or oversimplifying water molecule contributions can significantly reduce the accuracy of docking simulations.

Purpose of the Study:

To develop and evaluate a multi-body docking program that explicitly incorporates key water molecules into protein-ligand binding simulations.
To improve the accuracy and efficiency of molecular docking by accounting for the dynamic influence of hydration.

Main Methods:

Developed a multi-body docking program utilizing the NSGA II multi-objective optimization algorithm.
Integrated a force-field-based, hydration-specific scoring function to estimate binding affinity.
Tested the program with fixed and variable numbers of key water molecules for optimization.

Main Results:

Achieved an 80.58% success rate for docking accuracy with ligands smaller than 2.0 Å when water molecule numbers were fixed.
Demonstrated good cross-docking accuracy and screening efficiency compared to existing programs.
Showcased comparable performance with variable numbers of water molecules, indicating flexibility and efficiency.

Conclusions:

The developed multi-body docking program effectively addresses the limitations of traditional methods by explicitly modeling water molecule participation in protein-ligand binding.
This approach offers a more accurate and reliable tool for computational drug discovery and molecular modeling.