{ "description": "Per-run results for the Crane Bioworks held-out nanobody:antigen validation. 5 complexes x 3 seeds. Predictions from ESMFold2, single sequence, no MSA, no template. Scored with DockQ 2.1.3 against the deposited structures, and with the canonical Dunbrack ipSAE on the saved PAE arrays.", "model": { "repository": "biohub/ESMFold2", "revision": "623490563d9e25221074976b586a303a4a1cc301" }, "dockq_bands": { "acceptable": 0.23, "medium": 0.49, "high": 0.8 }, "training_cutoff": "2021-09", "runs": [ { "pdb": "9H1F", "antigen": "Cofilin-1", "deposited": "2024-10-09", "released": "2025-03-19", "seed": 0, "iptm": 0.8834, "ptm": 0.8856, "mean_plddt": 87.63, "dockq": 0.916279, "fnat": 0.904762, "irmsd": 0.5759, "lrmsd": 1.4283, "ipsae": 0.7266, "ipsae_d0chn": 0.8617, "interface_residues": 116 }, { "pdb": "9H1F", "antigen": "Cofilin-1", "deposited": "2024-10-09", "released": "2025-03-19", "seed": 1, "iptm": 0.8721, "ptm": 0.881, "mean_plddt": 87.24, "dockq": 0.909447, "fnat": 0.880952, "irmsd": 0.6099, "lrmsd": 0.8858, "ipsae": 0.682, "ipsae_d0chn": 0.8348, "interface_residues": 116 }, { "pdb": "9H1F", "antigen": "Cofilin-1", "deposited": "2024-10-09", "released": "2025-03-19", "seed": 2, "iptm": 0.876, "ptm": 0.8817, "mean_plddt": 87.53, "dockq": 0.923267, "fnat": 0.928571, "irmsd": 0.5729, "lrmsd": 1.5323, "ipsae": 0.6994, "ipsae_d0chn": 0.8456, "interface_residues": 116 }, { "pdb": "9LAD", "antigen": "Neuronal pentraxin-2", "deposited": "2025-01-02", "released": "2025-12-10", "seed": 0, "iptm": 0.8872, "ptm": 0.9227, "mean_plddt": 90.93, "dockq": 0.88891, "fnat": 0.957447, "irmsd": 0.8145, "lrmsd": 2.2045, "ipsae": 0.8333, "ipsae_d0chn": 0.9051, "interface_residues": 214 }, { "pdb": "9LAD", "antigen": "Neuronal pentraxin-2", "deposited": "2025-01-02", "released": "2025-12-10", "seed": 1, "iptm": 0.8883, "ptm": 0.9227, "mean_plddt": 90.95, "dockq": 0.866267, "fnat": 0.957447, "irmsd": 0.8744, "lrmsd": 2.9119, "ipsae": 0.8356, "ipsae_d0chn": 0.9064, "interface_residues": 214 }, { "pdb": "9LAD", "antigen": "Neuronal pentraxin-2", "deposited": "2025-01-02", "released": "2025-12-10", "seed": 2, "iptm": 0.8862, "ptm": 0.9236, "mean_plddt": 90.97, "dockq": 0.864919, "fnat": 0.93617, "irmsd": 0.8908, "lrmsd": 2.5179, "ipsae": 0.8325, "ipsae_d0chn": 0.9034, "interface_residues": 215 }, { "pdb": "9VWO", "antigen": "Oncostatin-M", "deposited": "2025-07-17", "released": "2026-07-22", "seed": 0, "iptm": 0.1727, "ptm": 0.5857, "mean_plddt": 81.61, "dockq": 0.034078, "fnat": 0.017241, "irmsd": 10.4729, "lrmsd": 32.2669, "ipsae": 0.0, "ipsae_d0chn": 0.0, "interface_residues": 0 }, { "pdb": "9VWO", "antigen": "Oncostatin-M", "deposited": "2025-07-17", "released": "2026-07-22", "seed": 1, "iptm": 0.1457, "ptm": 0.5731, "mean_plddt": 81.8, "dockq": 0.027568, "fnat": 0, "irmsd": 9.2065, "lrmsd": 34.623, "ipsae": 0.0, "ipsae_d0chn": 0.0, "interface_residues": 0 }, { "pdb": "9VWO", "antigen": "Oncostatin-M", "deposited": "2025-07-17", "released": "2026-07-22", "seed": 2, "iptm": 0.7787, "ptm": 0.8398, "mean_plddt": 86.3, "dockq": 0.823006, "fnat": 0.775862, "irmsd": 0.7806, "lrmsd": 2.7337, "ipsae": 0.5116, "ipsae_d0chn": 0.643, "interface_residues": 165 }, { "pdb": "9UO0", "antigen": "Spike glycoprotein", "deposited": "2025-04-24", "released": "2026-04-29", "seed": 0, "iptm": 0.4762, "ptm": 0.5074, "mean_plddt": 59.15, "dockq": 0.289616, "fnat": 0.660377, "irmsd": 5.7917, "lrmsd": 20.5898, "ipsae": 0.0585, "ipsae_d0chn": 0.4284, "interface_residues": 42 }, { "pdb": "9UO0", "antigen": "Spike glycoprotein", "deposited": "2025-04-24", "released": "2026-04-29", "seed": 1, "iptm": 0.5471, "ptm": 0.5254, "mean_plddt": 59.53, "dockq": 0.276559, "fnat": 0.603774, "irmsd": 6.2896, "lrmsd": 18.6438, "ipsae": 0.1262, "ipsae_d0chn": 0.4614, "interface_residues": 77 }, { "pdb": "9UO0", "antigen": "Spike glycoprotein", "deposited": "2025-04-24", "released": "2026-04-29", "seed": 2, "iptm": 0.3013, "ptm": 0.4563, "mean_plddt": 55.6, "dockq": 0.222172, "fnat": 0.528302, "irmsd": 9.2526, "lrmsd": 23.8614, "ipsae": 0.0139, "ipsae_d0chn": 0.3911, "interface_residues": 1 }, { "pdb": "9E7O", "antigen": "Gametocyte surface protein P230", "deposited": "2024-11-03", "released": "2025-07-30", "seed": 0, "iptm": 0.1016, "ptm": 0.4634, "mean_plddt": 72.36, "dockq": 0.067433, "fnat": 0.026316, "irmsd": 8.5244, "lrmsd": 20.5618, "ipsae": 0.0, "ipsae_d0chn": 0.0, "interface_residues": 0 }, { "pdb": "9E7O", "antigen": "Gametocyte surface protein P230", "deposited": "2024-11-03", "released": "2025-07-30", "seed": 1, "iptm": 0.0928, "ptm": 0.4346, "mean_plddt": 72.44, "dockq": 0.047, "fnat": 0.052632, "irmsd": 12.9578, "lrmsd": 29.8199, "ipsae": 0.0, "ipsae_d0chn": 0.0, "interface_residues": 0 }, { "pdb": "9E7O", "antigen": "Gametocyte surface protein P230", "deposited": "2024-11-03", "released": "2025-07-30", "seed": 2, "iptm": 0.1098, "ptm": 0.4552, "mean_plddt": 72.51, "dockq": 0.00644, "fnat": 0, "irmsd": 23.5142, "lrmsd": 68.2657, "ipsae": 0.0, "ipsae_d0chn": 0.0, "interface_residues": 0 } ], "confidence_metrics": { "iptm": "Inter-chain predicted TM score as reported by ESMFold2; it measures confidence in the relative arrangement of the chains, not their individual folds.", "ipsae": "Canonical ipSAE (Dunbrack 2025, bioRxiv 2025.02.10.637595), computed with ipsae.py from the saved PAE arrays. Convention: d0res, `max` row, PAE cutoff 10 A, distance cutoff 15 A.", "ipsae_d0chn": "The d0chn variant of ipSAE, reported because the variants spread by up to 0.14 on these runs.", "interface_residues": "n0res from ipsae.py: the partner-chain residue count below the PAE cutoff for the alignment residue and direction that maximize ipSAE, used for d0res normalization. This is not a total interface or residue-pair count. Zero means no inter-chain PAE pair passed the cutoff." } }