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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...
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-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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Updated: May 24, 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

Flexible protein-ligand docking using the Fleksy protocol.

Markus Wagener1, Jacob de Vlieg, Sander B Nabuurs

  • 1Department of Molecular Design and Informatics, MSD, Oss, The Netherlands.

Journal of Computational Chemistry
|February 29, 2012
PubMed
Summary
This summary is machine-generated.

This study introduces Fleksy, a new flexible docking tool. Fleksy accounts for protein and ligand flexibility to improve predictions of protein-ligand complex structures.

Keywords:
dockinginduced fitligandmodelingprotein

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05:08

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 Biology
  • Structural Biology
  • Drug Discovery

Background:

  • Accurate prediction of protein-ligand complex geometry is crucial for drug discovery.
  • Protein plasticity, or the ability of proteins to change shape, significantly impacts binding interactions.
  • Existing docking tools often struggle to fully account for both protein and ligand flexibility.

Purpose of the Study:

  • To introduce the first public release of Fleksy, a novel flexible docking software.
  • To enable simultaneous consideration of protein and ligand flexibility in molecular docking.
  • To provide a detailed description of Fleksy's workflow and features.

Main Methods:

  • Development of a flexible docking tool named Fleksy.
  • Integration of algorithms to model both protein and ligand conformational changes during docking.
  • Evaluation of Fleksy's performance using two established cross-docking benchmark datasets.

Main Results:

  • Fleksy successfully incorporates both protein and ligand flexibility into the docking process.
  • Performance assessment on benchmark datasets demonstrates the tool's capability in predicting complex geometries.
  • The software's workflow and features are detailed for user implementation.

Conclusions:

  • Fleksy represents a significant advancement in flexible docking methodologies.
  • Accounting for protein plasticity is essential for accurate protein-ligand complex modeling.
  • The release of Fleksy provides researchers with a powerful new tool for structural and drug discovery studies.