ArticleJournal of chemical information and modeling2024
Understanding and Quantifying Molecular Flexibility: Torsion Angular Bin Strings.
Article in Journal of chemical information and modeling, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Anisotropic NMR as a Crucial Tool for Differentiation of Epimers With High Conformational Flexibility.Angewandte Chemie (International ed. in English) · 2026Article
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- Torsion angular bin strings: algorithmic update and additional validation.Journal of cheminformatics · 2026Article
- eRMSF: A Python Package for Ensemble-Based RMSF Analysis of Biomolecular Systems.Journal of chemical information and modeling · 2025Article
- Molecular dynamics simulation of polymerization kinetics, dimensional stability, and in silico toxicity of nextgeneration silicone impression materials in dentistry.Journal of materials science. Materials in medicine · 2025Article
- Transferring Knowledge from MM to QM: A Graph Neural Network-Based Implicit Solvent Model for Small Organic Molecules.Journal of chemical theory and computation · 2025Article
- Rapid Access to Small Molecule Conformational Ensembles in Organic Solvents Enabled by Graph Neural Network-Based Implicit Solvent Model.Journal of the American Chemical Society · 2025Article
- Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization.Journal of cheminformatics · 2024Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular flexibility is a commonly used, but not easily quantified term. It is at the core of understanding composition and size of a conformational ensemble and contributes to many molecular properties. For many computational workflows, it is necessary to reduce a conformational ensemble to meaningful representatives, however defining them and guaranteeing the ensemble's completeness is difficult. We introduce the concepts of torsion angular bin strings (TABS) as a discrete vector representation of a conformer's dihedral angles and the number of possible TABS (nTABS) as an estimation for the ensemble size of a molecule, respectively. Here, we show that nTABS corresponds to an upper limit for the size of the conformational space of small molecules and compare the classification of conformer ensembles by TABS with classifications by RMSD. Overcoming known drawbacks like the molecular size dependency and threshold picking of the RMSD measure, TABS is shown to meaningfully discretize the conformational space and hence allows e.g. for fast checks of the coverage of the conformational space. The current proof-of-concept implementation is based on the ETKDGv3 conformer generator as implemented in the RDKit and known torsion preferences extracted from small-molecule crystallographic data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.