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Related Concept Videos

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...
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...
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...
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: Jun 7, 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

Docking validation resources: protein family and ligand flexibility experiments.

Sudipto Mukherjee1, Trent E Balius, Robert C Rizzo

  • 1Department of Applied Mathematics and Statistics, and Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, New York 11794, USA.

Journal of Chemical Information and Modeling
|November 2, 2010
PubMed
Summary

The SB2010 database evaluates molecular docking protocols for ligand-receptor complexes. Success rates vary by protocol and ligand flexibility, with scoring failures being more common than sampling issues.

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

Published on: June 20, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate prediction of ligand-bound conformations is crucial for virtual screening.
  • Existing docking protocols require rigorous evaluation across diverse ligand and protein types.
  • The SB2010 database provides a standardized resource for assessing docking performance.

Purpose of the Study:

  • To evaluate the accuracy of different molecular docking protocols (rigid, fixed anchor, flexible) using the SB2010 database.
  • To analyze the impact of ligand flexibility and protein family on docking success rates.
  • To identify common failure modes (scoring vs. sampling) in docking simulations.

Main Methods:

  • A database of 780 ligand-receptor complexes (SB2010) was compiled from the Protein Data Bank.
  • Three docking protocols within the DOCK program were tested: rigid (RGD), fixed anchor (FAD), and flexible (FLX).
  • Performance was assessed using metrics including global results, ligand flexibility, protein family, and cross-docking analysis.

Main Results:

  • Overall success rates: RGD (82.3%) > FAD (78.1%) > FLX (63.8%).
  • Success rates decreased with increasing ligand flexibility, particularly for FAD and FLX protocols.
  • Failures were predominantly due to scoring issues rather than sampling limitations.
  • Protein family, such as zinc-containing proteins, significantly influenced success rates, independent of ligand flexibility.

Conclusions:

  • The SB2010 database serves as a valuable community resource for improving docking protocols.
  • Ligand flexibility poses a significant challenge, especially for highly flexible molecules.
  • Understanding protein-specific binding site environments is critical for optimizing virtual screening strategies.