ArticleJournal of chemical information and modeling2025
Essential Considerations for Free Energy Calculations of RNA-Small Molecule Complexes: Lessons from the Theophylline-Binding RNA Aptamer.
Article in Journal of chemical information and modeling, 2025. 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.
- Fully Automatable Relative Binding Free Energy Calculations with Enhanced Sampling Using FAST/MBAR.Journal of chemical theory and computation · 2026Article
- Assessing Molecular Dynamics in Predicting Aptamer-Ligand Binding Thermodynamics: Insights from the OTA Binding Aptamers.Journal of chemical information and modeling · 2026Article
- Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1.Journal of chemical information and modeling · 2026Article
- Therapeutic rewiring of ceRNA networks: a computational pipeline for drug repurposing in acute kidney injury via circRNA-miRNA-mRNA axis disruption.Human genomics · 2026Review
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Streamlined Fragment-Based Discovery Platform for Targeting Structured RNAs.ACS chemical biology · 2025Article
- Path-Based Nonequilibrium Binding Free Energy Estimation, from Protein-Ligand to RNA-Ligand Binding.Journal of chemical information and modeling · 2025Article
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.Journal of chemical information and modeling · 2024Article
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Authors and funding
5 authors.
Funding
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Abstract
Alchemical free energy calculations are widely used to predict the binding affinity of small molecule ligands to protein targets; however, the application of these methods to RNA targets has not been deeply explored. We systematically investigated how modeling decisions affect the performance of absolute binding free energy calculations for a relatively simple RNA model system: theophylline-binding RNA aptamer with theophylline and five analogs. The goal of this investigation was 2-fold: (1) understanding the performance levels we can expect from absolute free energy calculations for a simple RNA complex and (2) learning about practical modeling considerations that impact the success of RNA-binding predictions, which may be different from the best practices established for protein targets. We learned that magnesium ion (Mg
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