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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...

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Modeling Ligands into Maps Derived from Electron Cryomicroscopy
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Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling.

Michal Brylinski1, Jeffrey Skolnick

  • 1Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, Georgia 30318, USA.

Journal of Computational Chemistry
|October 15, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces Q-Dock(LHM), a novel method for predicting ligand-binding poses. It accurately refines poses from ligand homology modeling, even with imperfect protein structures, enabling large-scale virtual screening.

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Area of Science:

  • Computational chemistry and structural biology.
  • Drug discovery and molecular modeling.

Background:

  • Ligand docking success relies heavily on receptor structure quality.
  • Advancements in protein structure prediction yield approximate models for many proteins.
  • Structure-based virtual screening needs efficient docking for theoretical models with inaccuracies.

Purpose of the Study:

  • To present Q-Dock(LHM), a low-resolution refinement method for ligand binding poses.
  • To evaluate Q-Dock(LHM) against classical docking approaches using experimental and theoretical receptor structures.
  • To demonstrate the utility of Q-Dock(LHM) for proteome-scale applications.

Main Methods:

  • Development of Q-Dock(LHM) for low-resolution refinement of binding poses.
  • Utilizing FINDSITE(LHM), a ligand homology modeling approach, to generate initial poses.
  • Comparative analysis of Q-Dock(LHM) against traditional docking methods on diverse receptor structures.

Main Results:

  • Q-Dock(LHM) demonstrates tolerance to receptor structure deformation, unlike all-atom docking.
  • The method achieves satisfactory performance in predicting ligand-binding poses.
  • Benchmarks show effectiveness across experimental (holo, apo) and theoretically modeled receptors.

Conclusions:

  • An evolution-based ligand homology modeling approach followed by fast, low-resolution refinement is effective for pose prediction.
  • Q-Dock(LHM) offers a promising solution for structure-based virtual screening against imperfect protein models.
  • The method shows potential for large-scale, proteome-wide drug discovery applications.