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Related Concept Videos

Ligand Binding Sites02:40

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 Sites02:40

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...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Conserved Binding Sites01:49

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 analyses the...
The Equilibrium Binding Constant and Binding Strength02:18

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:
Drug Discovery: Overview01:26

Drug Discovery: Overview

Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...

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Related Experiment Video

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Protein Target Prediction and Validation of Small Molecule Compound
10:21

Protein Target Prediction and Validation of Small Molecule Compound

Published on: February 23, 2024

Bioinformatics based Ligand-Docking and in-silico screening.

Daisuke Takaya1, Mayuko Takeda-Shitaka, Genki Terashi

  • 1School of Pharmacy, Kitasato University, Tokyo, Japan.

Chemical & Pharmaceutical Bulletin
|May 3, 2008
PubMed
Summary
This summary is machine-generated.

We introduce ChooseLD, a new bioinformatics method for flexible protein-ligand docking. It uses simulated annealing and a fingerprint alignment score to accurately predict drug-target interactions for drug discovery.

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Area of Science:

  • Computational chemistry
  • Bioinformatics
  • Drug discovery

Background:

  • Protein-ligand docking is crucial for identifying drug candidates.
  • Existing methods often struggle with flexible docking and accurate scoring.
  • Efficient and accurate docking methods are needed to accelerate drug development.

Purpose of the Study:

  • To develop a novel, accurate, and efficient computational method for protein-ligand flexible docking.
  • To introduce the ChooseLD (CHOOse biological information Semi-Empirically on the Ligand Docking) method.
  • To enhance the prediction of ligand binding conformations.

Main Methods:

  • Utilized simulated annealing (SA) for flexible docking.
  • Employed bioinformatics approaches for scoring.
  • Developed the fingerprint alignment score (FPAScore) to evaluate docking conformations.
  • Incorporated Metropolis Monte Carlo method for FPAScore optimization.
  • Calculated root mean square deviation (rmsd) of chemical descriptor atom coordinates.

Main Results:

  • Successfully developed and implemented the ChooseLD method.
  • Demonstrated the utility of FPAScore for determining accurate docking conformations.
  • The method integrates chemical descriptor matching (fingerprints) and coordinate analysis.
  • Optimized rigid body translation and rotation using Monte Carlo simulations.

Conclusions:

  • The ChooseLD method offers a novel approach to protein-ligand flexible docking.
  • This method has significant potential for applications in drug discovery and development.
  • ChooseLD can improve the identification of new drug candidates targeting disease-related proteins.