Structural Characterization and Ligand Binding Analysis of the Pan-Coronavirus Conserved G-Quadruplex: Implications for Broad-Spectrum Antiviral Drug Design

Computational workflow, scripts, and data for modeling pan-coronavirus conserved RNA G-quadruplex (G4) structures and analyzing their interactions with G4-stabilizing ligands. This dataset includes: - Template-based G4 structure modeling (based on PDB 6JJH) - All-atom Metropolis Monte Carlo (MM-MCMC) conformational sampling - AutoDock Vina molecular docking for berberine, PDS, and topotecan - AMBER MD simulations (100 ns × 3 independent replicas per system) - MM-GBSA binding free energy calculations (3 replicas) Key findings: - Apo G4: RMSD 5.49 ± 1.15 Å, Rg 10.33 ± 0.68 Å - Berberine-bound: ΔG = −25.2 ± 11.4 kcal/mol - PDS-bound: ΔG = −47.7 ± 6.2 kcal/mol Associated with the manuscript submitted to Journal of Chemical Information and Modeling (JCIM).