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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...
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...
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...
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:

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Related Experiment Video

Updated: Jul 9, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

High quality binding modes in docking ligands to proteins.

Boris Gorelik1, Amiram Goldblum

  • 1Department of Medicinal Chemistry and Natural Products and the David R. Bloom Center for Pharmacy, School of Pharmacy, Hebrew University of Jerusalem, Israel 91120.

Proteins
|December 7, 2007
PubMed
Summary

ISE-dock, a new protein-ligand docking program, generates multiple near-optimal conformations for improved biomolecular interaction accuracy. It outperforms existing methods in finding accurate docking poses efficiently.

Related Experiment Videos

Last Updated: Jul 9, 2026

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach
10:01

Structure-Guided Design and Development of Novel Cyclophilin A Inhibitors and Ganoderiol-F Derivatives: An In-Silico Approach

Published on: June 23, 2026

Area of Science:

  • Computational Biology
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate representation of protein-ligand interactions is crucial for drug discovery.
  • Traditional docking methods often rely on single conformations, potentially missing optimal binding poses.

Purpose of the Study:

  • To introduce ISE-dock, a novel docking program utilizing the Iterative Stochastic Elimination (ISE) algorithm.
  • To evaluate ISE-dock's performance in generating multiple near-optimal docking poses for protein-ligand complexes.

Main Methods:

  • Development of the ISE-dock program based on the ISE algorithm for pose generation.
  • Validation using 81 protein-ligand complexes from the Protein Data Bank (PDB).
  • Comparative performance analysis against Glide, GOLD, and AutoDock using RMSD metrics and paired t-tests.

Main Results:

  • ISE-dock generates large sets of near-optimal poses at no extra computational cost.
  • Achieved higher accuracy than Glide, GOLD, and AutoDock, with >60% top poses within 2.0 Å RMSD and >80% within 3.0 Å RMSD.
  • In 98% of cases, ISE-dock produced solutions within 2.0 Å of experimental poses and provided over 100-fold more solutions than AutoDock's LGA in comparable time.

Conclusions:

  • ISE-dock offers a significant advantage in accurately representing biomolecular interactions by providing multiple near-optimal conformations.
  • The program demonstrates superior performance and efficiency compared to existing docking tools.
  • The utility of large near-optimal pose populations is highlighted by correlations with experimental data supporting multiple binding modes.