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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...
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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Related Experiment Video

Updated: May 31, 2026

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
09:30

Modeling Ligands into Maps Derived from Electron Cryomicroscopy

Published on: July 19, 2024

Scalable Ligand Pose Generation via QUBO-Guided Grid Sampling and Geometric Triplet Matching.

Pei-Kun Yang1

  • 1Independent Researcher, Hsinchu 300, Taiwan.

Journal of Chemical Information and Modeling
|May 28, 2026
PubMed
Summary

This study introduces a novel Quadratic Unconstrained Binary Optimization (QUBO) framework for efficient ligand pose generation in drug discovery. The method offers a scalable and flexible approach for structure-based virtual screening, achieving performance comparable to existing docking programs.

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Last Updated: May 31, 2026

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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Drug Discovery

Background:

  • Structure-based virtual screening is crucial for identifying potential drug candidates.
  • Efficient and accurate ligand pose generation is a key challenge in virtual screening.

Purpose of the Study:

  • To develop a scalable framework for ligand pose generation using Quadratic Unconstrained Binary Optimization (QUBO).
  • To provide a modular approach for generating physically plausible ligand poses for virtual screening.

Main Methods:

  • Discretizing protein binding pockets into 3D grids.
  • Formulating and optimizing a QUBO model to identify favorable grid points.
  • Generating ligand poses by aligning ligand atom triplets to grid-point triplets.

Main Results:

  • The QUBO framework demonstrated comparable pose-recovery performance to established docking programs like AutoDock4 and Vina.
  • Increasing candidate pose numbers improved the inclusion of near-native poses.
  • Steric-clash filtering effectively reduced the size of the candidate-pose set.

Conclusions:

  • QUBO-guided grid sampling offers a scalable and flexible method for ligand pose generation.
  • The proposed framework integrates seamlessly into modern virtual screening workflows.
  • This approach enhances the efficiency of structure-based drug discovery.