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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...
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...

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Updated: May 9, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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PockFlex: a web server for flexibility-aware binding site identification and prioritisation from structural

Inés S Rahali1, Yacine Serir2, Kheira Rahali2

  • 1Inserm U1133, CNRS UMR 8251, Université Paris Cité, Rue Hélène Brion, 75013 Paris, France.

Nucleic Acids Research
|May 8, 2026
PubMed
Summary

PockFlex analyzes protein binding sites in structural ensembles, identifying recurring pockets and their druggability. This tool aids in characterizing and prioritizing stable binding sites across various protein conformations.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Drug Discovery

Background:

  • Protein structural ensembles capture dynamic conformational changes crucial for function and drug interactions.
  • Identifying and characterizing stable binding sites within these ensembles is challenging but essential for drug discovery.

Purpose of the Study:

  • To develop and present PockFlex, a web server for analyzing protein binding pockets across structural ensembles.
  • To enable the characterization, reconstruction, and prioritization of recurrent binding site organizations.

Main Methods:

  • PockFlex detects pockets in individual conformations and groups them based on residue similarity across the ensemble.
  • A residue-centered clustering framework identifies persistent and transient binding site regions.
  • Pocket druggability is assessed using the PockDrug workflow and summarized at the cluster level.

Main Results:

  • The server successfully identifies recurrent binding site clusters within protein structural ensembles.
  • It quantifies residue recurrence and variability, distinguishing stable from dynamic binding regions.
  • Druggability is evaluated considering conformational variability, aiding in site prioritization.

Conclusions:

  • PockFlex provides interactive, residue-level insights into binding site dynamics and druggability.
  • The tool supports the prioritization of drug targets by characterizing stable binding pockets in flexible proteins.
  • PockFlex is freely accessible, facilitating research in structural biology and drug discovery.