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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...
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:
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...
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
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Published on: July 25, 2013

Two-dimensional replica-exchange method for predicting protein-ligand binding structures.

Hironori Kokubo1, Toshimasa Tanaka, Yuko Okamoto

  • 1Pharmaceutical Research Division, Medicinal Chemistry Research Laboratories, Takeda Pharmaceutical Co., Ltd., 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-8585, Japan.

Journal of Computational Chemistry
|September 6, 2013
PubMed
Summary
This summary is machine-generated.

A new two-dimensional replica-exchange method enhances protein-ligand binding structure prediction. This improved sampling efficiency accurately determines binding poses faster than previous methods.

Keywords:
computer-aided drug designmolecular dynamicsprotein-ligand bindingreplica exchange with solute temperingreplica-exchange umbrella samplingstructure prediction

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Biophysics

Background:

  • Predicting protein-ligand binding structures is crucial for drug discovery.
  • Accurate prediction requires efficient conformational sampling of molecular interactions.

Purpose of the Study:

  • To develop a novel two-dimensional replica-exchange method for enhanced protein-ligand binding structure prediction.
  • To improve sampling efficiency and speed up the prediction process.

Main Methods:

  • A two-dimensional replica-exchange method combining umbrella sampling and solute tempering.
  • Umbrella sampling along the distance between protein binding pocket and ligand.
  • Solute tempering to weaken ligand-protein and ligand-water interactions, facilitating ligand movement.

Main Results:

  • The method successfully predicted ligand binding structures for MDM2 and HSP 90-alpha systems.
  • Predicted structures showed excellent agreement with experimental data from the Protein Data Bank.
  • Achieved significantly faster prediction times compared to previous replica-exchange umbrella sampling methods due to improved sampling efficiency.

Conclusions:

  • The developed two-dimensional replica-exchange method is a highly efficient approach for protein-ligand binding structure prediction.
  • This method offers a faster and more accurate alternative for determining binding poses, advancing computational drug design.