OpenFold3 MCL1 protein-ligand ensemble predictions (20 structures) on SDSC Expanse V100

Ensemble of 20 AlphaFold3-equivalent structure predictions of the MCL1 protein-ligand complex (official OpenFold3 example, PDB 5FDR context), generated with OpenFold3 0.4.5 on a single NVIDIA V100 32GB GPU on SDSC Expanse (job 53383743, 24min13s). 4 seeds (42,1337,2024,2026) x 5 diffusion samples, real MSAs (ColabFold server). Includes: 20 model PDBs (protein chains A-D + ATP ligands F/G/H + small-molecule ligand Z), per-atom and aggregated confidence JSONs (avg_plddt, ptm, iptm, bespoke_iptm, sample_ranking_score), timing, plus the ensemble confidence-vs-ligand-pose-consistency analysis (corr(sample_ranking_score, ligand RMSD) = -0.58). Analysis: confidence ranking correlates with ligand-pose consistency. Reproducible scripts: github.com/zonca/openfold3-mcl1-expanse