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Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings.

Jessica Braun1, Paul Katzberger1, Gregory A Landrum1

  • 1Department of Chemistry and Applied Biosciences, ETH Zurich Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland.

Journal of Chemical Information and Modeling
|October 10, 2024
PubMed
Summary
This summary is machine-generated.

We introduce torsion angular bin strings (TABS) to quantify molecular flexibility. This new method estimates conformational ensemble size and discretizes molecular conformational space more effectively than RMSD.

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Area of Science:

  • Computational chemistry
  • Molecular modeling
  • Structural biology

Background:

  • Molecular flexibility is crucial for understanding molecular properties and conformational ensembles.
  • Quantifying molecular flexibility and representing conformational space are challenging in computational chemistry.
  • Existing methods like RMSD have limitations in discretizing conformational space.

Purpose of the Study:

  • To introduce torsion angular bin strings (TABS) as a novel discrete vector representation for conformers.
  • To propose nTABS as a method for estimating the size of a molecule's conformational ensemble.
  • To demonstrate TABS's advantages over RMSD for discretizing conformational space and assessing ensemble completeness.

Main Methods:

  • Developed TABS, a discrete vector representation based on dihedral angles.
  • Utilized the ETKDGv3 conformer generator from RDKit for generating conformers.
  • Incorporated torsion preferences from small-molecule crystallographic data.
  • Compared TABS classification of conformer ensembles with RMSD-based classification.

Main Results:

  • nTABS provides an upper limit estimation for the conformational space size of small molecules.
  • TABS effectively discretizes conformational space, overcoming RMSD's limitations like molecular size dependency and threshold picking.
  • TABS allows for rapid checks of conformational space coverage.

Conclusions:

  • TABS offers a robust and meaningful way to discretize molecular conformational space.
  • This method enhances the analysis of conformational ensembles in computational chemistry.
  • TABS provides a valuable tool for assessing the completeness of generated conformer sets.