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Junior B. 9efdc0acf1 Pose-RMSD confirms HDAC2/vorinostat geometry: 0.21A (Vina was 7.9A)

Close the §12.4 validation loop. scripts/pose_rmsd.py superposes the
Boltz-2-predicted HDAC2 onto crystal 4LXZ, transforms the predicted
ligand, and scores pose RMSD (spyrmsd, in-place):
- protein fold: Ca RMSD 0.14A over 366 residues
- vorinostat pose: 0.21A (crystal-accurate) vs Vina 7.9A on this exact
  Zn-chelation case
- catalytic Zn ion: 2.73A off (ligand perfect, metal slightly less)

HDAC2 now validated on BOTH affinity (P(binder)=0.999) and geometry
(0.21A). The structure-binding modality is comprehensively validated on
its decisive metal-coordination case. Commits the predicted complex as
evidence (docs/results/HDAC2_vorinostat_pred.pdb).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

2026-06-24 19:50:33 +02:00

binding_ligand_baseline.py

Structure-binding track: scaffold + ligand-retrieval baseline

2026-06-23 23:53:27 +02:00

dock_positive_controls.py

Docking baseline: toolchain solved, raw affinity is size-biased

2026-06-24 00:03:00 +02:00

dock_production.py

Production docking: prep helps (7.9->4.8A) but Vina wrong tool for sickle

2026-06-24 16:38:54 +02:00

dock_validate.py

Redocking-RMSD validation fails 3/3: pipeline-quality issue