Context-dependent geometric variability of HIV-1 Env glycan sites

This preprint evaluates ensemble geometric persistence (EGP), a protein-backbone geometric-variability descriptor of HIV-1 Env glycosylation-site neighborhoods. Across the original 15-structure discovery and six-structure external panels, independently frozen discovery scores yielded a site-rank Spearman correlation of 0.791 (19 sites). In a five-structure BG505 holdout, the corresponding correlation weakened to 0.340 (20 sites; nominal p = 0.143). Protomer-consistent sensitivity analyses and a nested partition of 572 fully observed site-neighbor measurements showed substantial dependence on structural sampling; 76.6% of pooled distance-deviation sums of squares arose between deposited structures. No predictive validity for biochemical occupancy or Endo H resistance is claimed. The accompanying archive provides the original structural inputs, analysis scripts, tabular outputs, figures, source manifest, and SHA-256 checksums.