ArticleRSC advances2026
Ensemble molecular dynamics for predicting binding energies of DNA intercalators.
Article in RSC advances, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Design, Synthesis, and Evaluation of a Novel Phenanthrene Derivative as a Potential DNA Intercalator.ACS chemical biology · 2026Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ensemble molecular dynamics (MD) simulations have been widely used to improve binding energy predictions in protein-ligand systems, but their application to DNA-ligand systems is limited. Following previous studies on DNA-doxorubicin and DNA-proflavine systems, the present study extends the ensemble MD simulations for a total of 16 intercalators spanning different molecular sizes, intercalating scaffolds, flexibilities, and charges. For each DNA-intercalator complex, 25 independent 10 ns MD replicas were simulated using randomized initial velocities. The uncorrected Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) energies significantly overestimated the binding energies and had a poor correlation with the corresponding experimental values (with a correlation coefficient
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Registered trials
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