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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...
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:
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:
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...
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...
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...

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Related Experiment Video

Updated: Jun 12, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Empirical potentials for ion binding in proteins.

Sergei Rahmanov1, Ivan Kulakovskiy, Leonid Uroshlev

  • 1Research Institute for Genetics and Selection of Industrial Microorganisms, Genetika, 1 Dorozhny proezd 1, Moscow 117545, Russia. sergeira@genetika.ru

Journal of Bioinformatics and Computational Biology
|June 18, 2010
PubMed
Summary
This summary is machine-generated.

Empirical potentials for protein-ion interactions were developed using statistical analysis of protein structures. These potentials accurately predict ion-binding sites, aiding in understanding protein function and drug discovery.

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Determination of the Gas-phase Acidities of Oligopeptides
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Determination of the Gas-phase Acidities of Oligopeptides

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Last Updated: Jun 12, 2026

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
06:50

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Quantifying the Binding Interactions Between Cu(II) and Peptide Residues in the Presence and Absence of Chromophores
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Determination of the Gas-phase Acidities of Oligopeptides
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Determination of the Gas-phase Acidities of Oligopeptides

Published on: June 24, 2013

Area of Science:

  • Biophysics
  • Computational Biology
  • Structural Biology

Background:

  • Understanding protein-ion interactions is crucial for cellular processes.
  • Accurate modeling of these interactions is essential for predicting protein function and designing therapeutics.

Purpose of the Study:

  • To develop and validate empirical potentials for protein-ion interactions.
  • To create a computational tool for predicting ion-binding sites in proteins.

Main Methods:

  • Utilized a large dataset from the Protein Data Bank (PDB).
  • Employed statistical analysis of ion-protein atom contacts.
  • Applied Monte Carlo Reference State simulations.

Main Results:

  • Derived detailed, continuous empirical potentials for protein-ion interactions.
  • Potentials accurately predict the location and specificity of ion-binding sites.
  • Achieved high accuracy in predicting known ion-binding sites.

Conclusions:

  • The developed empirical potentials provide a robust method for studying protein-ion interactions.
  • The web server facilitates accurate prediction of ion-binding sites, aiding further research.