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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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Conserved Binding Sites

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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.
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...
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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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The Equilibrium Binding Constant and Binding Strength02:18

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The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
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Protein-protein Interfaces

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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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Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
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CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction.

Mingwei Pang1, Wangqiu He1, Xufeng Lu2

  • 1Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, Jiangsu, China.

BMC Bioinformatics
|November 23, 2023
PubMed
Summary

The CoDock-Ligand method combines template-based modeling and the GNINA scoring function for accurate ligand binding prediction. This hybrid approach achieved successful predictions for most targets in the CASP15 competition.

Keywords:
CASPCoDock-LigandLigand binding predictionMolecular docking

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Drug discovery

Background:

  • Accurate ligand binding prediction is essential for molecular docking.
  • Integrating template-based modeling with precise scoring functions is crucial.

Purpose of the Study:

  • To introduce the CoDock-Ligand docking method for ligand binding prediction.
  • To evaluate the performance of CoDock-Ligand in the CASP15 competition.

Main Methods:

  • CoDock-Ligand combines template-based modeling with the GNINA scoring function (a Convolutional Neural Network-based function).
  • The method was applied to ligand binding prediction tasks in CASP15.

Main Results:

  • Successful predictions were achieved for 14 out of 21 CASP15 targets within the top 5 submissions.
  • Partially successful predictions were obtained for 4 additional targets.
  • The method accurately predicted the binding of most ligands for the complex H1114 target, featuring 56 metal cofactors and small molecules.

Conclusions:

  • The hybrid CoDock-Ligand docking scheme effectively addresses ligand binding prediction challenges.
  • Conformational changes in receptor proteins can impact prediction accuracy, highlighting areas for future improvement.