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Related Concept Videos

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:
Ligand Binding and Linkage00:49

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 the...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...

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Related Experiment Video

Updated: Jul 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

Published on: June 20, 2025

Empirical entropic contributions in computational docking: evaluation in APS reductase complexes.

Max W Chang1, Richard K Belew, Kate S Carroll

  • 1Bioinformatics Program, University of California at San Diego, La Jolla, California 92093, USA.

Journal of Computational Chemistry
|March 21, 2008
PubMed
Summary

Evaluating binding entropy in ligand-protein complexes can be achieved through reiterated docking. A simple cluster size method effectively identified correct conformations for nucleotide analogues binding to APS reductase.

Related Experiment Videos

Last Updated: Jul 6, 2026

Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
08:49

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
  • Biochemistry
  • Molecular modeling

Background:

  • Accurate estimation of binding entropy is crucial for understanding ligand-protein interactions.
  • Vibrational entropy contributes significantly to the overall binding free energy.
  • Assessing this contribution computationally remains a challenge.

Purpose of the Study:

  • To evaluate empirical methods for calculating the vibrational entropy of binding.
  • To test the performance of different computational approaches using nucleotide analogues and APS reductase.
  • To identify the most effective method for analyzing docking experiment results.

Main Methods:

  • Utilized reiterated docking experiments to assess ligand-protein complexes.
  • Applied cluster size methods to measure conformational probabilities.
  • Employed RMSD-based methods to analyze the scatter and clustering of conformations.
  • Directly characterized the energy landscape by random sampling around docked poses.

Main Results:

  • Compared the performance of several methods for evaluating vibrational entropy.
  • The simple cluster size method demonstrated superior performance.
  • This method improved the identification of correct ligand conformations in multiple docking experiments.
  • Tested on 22 nucleotide analogues binding to APS reductase.

Conclusions:

  • Reiterated docking experiments provide a viable approach for evaluating empirical vibrational entropy.
  • The simple cluster size method is a promising technique for improving the accuracy of molecular docking.
  • This finding has implications for drug discovery and understanding enzyme mechanisms.