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

The Equilibrium Binding Constant and Binding Strength

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:
Protein-protein Interfaces02:04

Protein-protein Interfaces

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 polypeptide...
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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Bootstrap-based consensus scoring method for protein-ligand docking.

Hiroaki Fukunishi1, Reiji Teramoto, Toshikazu Takada

  • 1Nano Electronics Research Laboratories, NEC Corporation, 34, Miyukigaoka, Tsukuba, Ibaraki 305-8501, Japan. h-fukunishi@bu.jp.nec.com

Journal of Chemical Information and Modeling
|April 23, 2008
PubMed
Summary
This summary is machine-generated.

Bootstrap-based consensus scoring (BBCS) enhances protein-ligand docking performance by combining multiple scoring functions. This ensemble learning method improves the accuracy of identifying correct protein-ligand complex structures.

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Protein Target Prediction and Validation of Small Molecule Compound
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Area of Science:

  • Computational Chemistry
  • Structural Biology
  • Bioinformatics

Background:

  • Protein-ligand docking is crucial for drug discovery.
  • Existing scoring functions often have limitations in accuracy.
  • Ensemble learning offers a promising approach to improve predictive models.

Purpose of the Study:

  • To develop and evaluate a novel consensus scoring method for protein-ligand docking.
  • To enhance the performance of single scoring functions using ensemble techniques.
  • To improve the accuracy of predicting native protein-ligand complex structures.

Main Methods:

  • Developed bootstrap-based consensus scoring (BBCS) using ensemble learning.
  • Generated multiple energy-parameter sets by optimizing against bootstrap-resampled training sets.
  • Applied Z-score optimization based on energy landscape theory.
  • Tested BBCS on the FlexX scoring function using 50 training and 48 independent complexes.

Main Results:

  • BBCS significantly improved the success rate of recognizing crystal structures compared to single scoring (33.3% to 52.1%).
  • The rank of crystal structures improved for 54.2% of complexes without worsening any.
  • BBCS outperformed conventional consensus scoring (CS).

Conclusions:

  • BBCS is an effective method for improving protein-ligand docking accuracy.
  • Ensemble learning, specifically BBCS, offers a robust strategy to enhance scoring function performance.
  • The developed method shows potential for advancing drug discovery efforts.