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Related Concept Videos

Chair Conformation of Cyclohexane02:02

Chair Conformation of Cyclohexane

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The chair conformation is the most stable form of cyclohexane due to the absence of angle and torsional strain. The absence of angle strain is a result of cyclohexane’s bond angle being very close to the ideal tetrahedral bond angle of 109.5° in its chair conformer. Similarly, the torsional strain is also absent owing to the perfectly staggered arrangement of bonds.
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Cyclohexane does not exist in a planar form due to the high angle and torsional strain it would experience in the planar structure. Instead, it adopts non-planar chair and boat conformations.
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In an organic molecule, free rotation about the carbon-carbon single bond results in energetically different conformers of the molecule. Due to this rotation, called the internal rotation, ethane has two major conformations — staggered and eclipsed.
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis
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Incorporating Target Protein Structure Flexibility and Dynamics in Computational Drug Discovery Using Ensemble-Based Docking Analysis

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Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy.

Yujin Wu1, Charles L Brooks1,2

  • 1Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.

Journal of Chemical Information and Modeling
|October 27, 2021
PubMed
Summary
This summary is machine-generated.

This study introduces a new flexible receptor docking method that accurately predicts ligand-protein binding modes by including side chain flexibility and entropic contributions. The enhanced algorithm improves docking accuracy and identifies lead compounds more effectively than existing rigid docking approaches.

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Area of Science:

  • Computational chemistry and molecular modeling.
  • Drug discovery and development.
  • Structural biology.

Background:

  • Predicting ligand-macromolecule binding modes is crucial for structure-based drug design.
  • Existing flexible docking methods often neglect side chain conformational entropy.
  • Accurate modeling of binding pockets requires accounting for receptor flexibility.

Purpose of the Study:

  • To develop a novel physics-based scoring function and hybrid search algorithm for flexible receptor docking.
  • To incorporate enthalpic and entropic contributions, including side chain conformational variability.
  • To improve the accuracy of predicting ligand binding modes and identifying potential drug candidates.

Main Methods:

  • Developed a new scoring function considering enthalpic and entropic contributions.
  • Implemented a hybrid search algorithm combining molecular dynamics (MD)-based simulated annealing and genetic algorithm crossovers.
  • Tested the algorithm on diverse protein targets (thrombin, DHFR, T4 L99A, PDE10A) and a riboswitch RNA target.
  • Evaluated performance on decoy sets (DUD-E) and compared with existing methods (DOCK, CDOCKER, AutoDock Vina).

Main Results:

  • Demonstrated improved accuracy in flexible cross-docking compared to rigid docking, with up to 23.64% improvement for DHFR ligands.
  • Showcased applicability to RNA docking with a riboswitch example.
  • Outperformed DOCK in modeling flexible binding site residues.
  • Achieved superior performance over rigid receptor CDOCKER and AutoDock Vina in distinguishing binders from nonbinders.
  • Validated the method's speed for potential high-throughput screening.

Conclusions:

  • The proposed flexible docking algorithm significantly enhances the accuracy of predicting ligand binding modes.
  • The method effectively models receptor flexibility and incorporates entropic contributions, leading to better performance.
  • Flexible CDOCKER shows promise for lead compound identification and can be utilized in high-throughput docking screens.