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Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

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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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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...
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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...
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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.
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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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Alloscore: a method for predicting allosteric ligand-protein interactions.

Shuai Li1, Qiancheng Shen1, Minyi Su2

  • 1Department of Pathophysiology, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China and.

Bioinformatics (Oxford, England)
|January 24, 2016
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Summary
This summary is machine-generated.

Allosteric ligands offer targeted therapy with fewer side effects. Alloscore is a new web server predicting allosteric ligand-protein binding affinities for drug discovery.

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Area of Science:

  • Medicinal Chemistry
  • Computational Biology
  • Pharmacology

Background:

  • Allosteric ligands are promising therapeutic agents due to enhanced target selectivity and reduced toxicity compared to orthosteric ligands.
  • Understanding allosteric ligand-protein interactions is crucial for developing novel allosteric drugs, representing a significant challenge in drug discovery.

Purpose of the Study:

  • To introduce Alloscore, a novel web server designed to predict the binding affinities of allosteric ligand-protein interactions.
  • To provide a computational tool to aid in the understanding and development of allosteric modulators.

Main Methods:

  • Development of the Alloscore web server utilizing a predictive method for allosteric binding affinities.
  • Validation of the method's performance in describing allosteric binding interactions.

Main Results:

  • The Alloscore method demonstrates prominent performance in predicting allosteric binding.
  • The developed web server provides a valuable resource for computational drug discovery.

Conclusions:

  • Alloscore is a powerful tool for virtual screening of allosteric drug candidates.
  • The server can facilitate the structural optimization of allosteric agonists and antagonists, advancing allosteric drug discovery efforts.