{ "engine": "bio-suite kabsch-tm-compare (3D Kabsch SO(3) SVD Superposition, Motif RMSD & Zhang-Skolnick TM-Score)", "benchmark_id": "TOOL-BENCHMARK-22-KABSCH-TMSCORE-VS-SCIPY", "validation_set_id": "VAL-SET-011-KABSCH-TMSCORE-PDB-12COHORT", "external_reference": "SciPy v1.18.1 (scipy.linalg.svd Kabsch SO(3)) + NumPy v2.5.4 + Zhang & Skolnick (2004) TM-Score", "total_cohorts": 12, "dev_cohorts": 6, "reserve_cohorts": 6, "dev_mean_backbone_rmsd_diff": 0.0, "reserve_mean_backbone_rmsd_diff": 0.0, "dev_mean_motif_rmsd_diff": 0.0, "reserve_mean_motif_rmsd_diff": 0.0, "dev_mean_tm_score_diff": 0.0, "reserve_mean_tm_score_diff": 0.0, "overall_rmsd_pearson_r": 1.0, "overall_tm_score_pearson_r": 1.0, "regime_concordance_pct": 100.0, "total_native_ms": 0.5195, "total_scipy_ms": 166.3289, "speedup_factor": 320.1711, "cohorts": [ { "cohort_id": "DEV-01", "split": "Development", "name": "Human HSP90-Alpha Bergerat ATPase Lid Motif Scaffold (PDB 1UYD)", "pdb_id": "1UYD", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.1054, "unguarded_improper_rmsd_angstrom": 0.7846, "native_motif_rmsd_angstrom": 0.3355, "scipy_motif_rmsd_angstrom": 0.3355, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.7846, "scipy_backbone_rmsd_angstrom": 0.7846, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9441, "scipy_tm_score": 0.9441, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.34 A, Backbone RMSD = 0.78 A, TM = 0.9441 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "DEV-02", "split": "Development", "name": "Human Bruton's Tyrosine Kinase BTK Catalytic Cleft Scaffold (PDB 6X3P)", "pdb_id": "6X3P", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.0283, "unguarded_improper_rmsd_angstrom": 0.9183, "native_motif_rmsd_angstrom": 0.425, "scipy_motif_rmsd_angstrom": 0.425, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.9183, "scipy_backbone_rmsd_angstrom": 0.9183, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9256, "scipy_tm_score": 0.9256, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.42 A, Backbone RMSD = 0.92 A, TM = 0.9256 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "DEV-03", "split": "Development", "name": "E. coli Dihydrofolate Reductase Met20 Loop Active-Site Scaffold (PDB 1RX2)", "pdb_id": "1RX2", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.1814, "unguarded_improper_rmsd_angstrom": 0.7086, "native_motif_rmsd_angstrom": 0.2674, "scipy_motif_rmsd_angstrom": 0.2674, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.7086, "scipy_backbone_rmsd_angstrom": 0.7086, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9538, "scipy_tm_score": 0.9538, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.27 A, Backbone RMSD = 0.71 A, TM = 0.9538 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "DEV-04", "split": "Development", "name": "K. pneumoniae SHV-1 Ser70 Oxyanion-Hole Triad Scaffold (PDB 4ZAM)", "pdb_id": "4ZAM", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.0572, "unguarded_improper_rmsd_angstrom": 0.8328, "native_motif_rmsd_angstrom": 0.4025, "scipy_motif_rmsd_angstrom": 0.4025, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.8328, "scipy_backbone_rmsd_angstrom": 0.8328, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9376, "scipy_tm_score": 0.9376, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.40 A, Backbone RMSD = 0.83 A, TM = 0.9376 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "DEV-05", "split": "Development", "name": "De Novo Kemp Eliminase HG4 TIM-Barrel Catalytic Clamp (PDB 5RGF)", "pdb_id": "5RGF", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.2771, "unguarded_improper_rmsd_angstrom": 0.6129, "native_motif_rmsd_angstrom": 0.2922, "scipy_motif_rmsd_angstrom": 0.2922, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.6129, "scipy_backbone_rmsd_angstrom": 0.6129, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9648, "scipy_tm_score": 0.9648, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.29 A, Backbone RMSD = 0.61 A, TM = 0.9648 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "DEV-06", "split": "Development", "name": "Unfolded Random-Walk Steric Decoy Control (0-Beaker Gate)", "pdb_id": "1ORC", "num_residues": 60, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 38.7891, "unguarded_improper_rmsd_angstrom": 39.606, "native_motif_rmsd_angstrom": 36.8432, "scipy_motif_rmsd_angstrom": 36.8432, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 39.6791, "scipy_backbone_rmsd_angstrom": 39.6791, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.0077, "scipy_tm_score": 0.0077, "abs_diff_tm_score": 0.0, "regime_classification": "0-Beaker Unfolded Random-Walk Control Rejected (RMSD = 39.68 A, TM = 0.0077 < 0.50)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-01", "split": "Reserve", "name": "Human Checkpoint Kinase 2 (CHK2) Hinge-Loop Motif Scaffold (PDB 4BDF)", "pdb_id": "4BDF", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.0903, "unguarded_improper_rmsd_angstrom": 0.7997, "native_motif_rmsd_angstrom": 0.358, "scipy_motif_rmsd_angstrom": 0.358, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.7997, "scipy_backbone_rmsd_angstrom": 0.7997, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9421, "scipy_tm_score": 0.9421, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.36 A, Backbone RMSD = 0.80 A, TM = 0.9421 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-02", "split": "Reserve", "name": "Human Estrogen Receptor Alpha (ESR1) Helix-12 Coactivator Clamp (PDB 1G50)", "pdb_id": "1G50", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.1724, "unguarded_improper_rmsd_angstrom": 0.7176, "native_motif_rmsd_angstrom": 0.3465, "scipy_motif_rmsd_angstrom": 0.3465, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.7176, "scipy_backbone_rmsd_angstrom": 0.7176, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9527, "scipy_tm_score": 0.9527, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.35 A, Backbone RMSD = 0.72 A, TM = 0.9527 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-03", "split": "Reserve", "name": "S. aureus Topoisomerase IV ParE GHKL ATP-Binding Motif (PDB 4URL)", "pdb_id": "4URL", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.0115, "unguarded_improper_rmsd_angstrom": 0.9015, "native_motif_rmsd_angstrom": 0.3719, "scipy_motif_rmsd_angstrom": 0.3719, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.9015, "scipy_backbone_rmsd_angstrom": 0.9015, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9281, "scipy_tm_score": 0.9281, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.37 A, Backbone RMSD = 0.90 A, TM = 0.9281 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-04", "split": "Reserve", "name": "Phage Lambda Cro Repressor Helix-Turn-Helix DNA-Binding Motif (PDB 1ORC)", "pdb_id": "1ORC", "num_residues": 64, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.2703, "unguarded_improper_rmsd_angstrom": 0.6197, "native_motif_rmsd_angstrom": 0.3103, "scipy_motif_rmsd_angstrom": 0.3103, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.6197, "scipy_backbone_rmsd_angstrom": 0.6197, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.9524, "scipy_tm_score": 0.9524, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.31 A, Backbone RMSD = 0.62 A, TM = 0.9524 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-05", "split": "Reserve", "name": "Telomeric G-Quadruplex Parallel Propeller Loop Scaffold (PDB 1XAV)", "pdb_id": "1XAV", "num_residues": 40, "clamped_motif_residues": 15, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 0.1397, "unguarded_improper_rmsd_angstrom": 0.7503, "native_motif_rmsd_angstrom": 0.3155, "scipy_motif_rmsd_angstrom": 0.3155, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 0.7503, "scipy_backbone_rmsd_angstrom": 0.7503, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.8656, "scipy_tm_score": 0.8656, "abs_diff_tm_score": 0.0, "regime_classification": "Active-Site Motif & Fold Validated (Motif RMSD = 0.32 A, Backbone RMSD = 0.75 A, TM = 0.8656 >= 0.85)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 }, { "cohort_id": "RES-06", "split": "Reserve", "name": "Chiral Mirror-Image D-Enantiomer Reflection Control (det(R)=+1 Guard, 0-Beaker Gate)", "pdb_id": "5RGF", "num_residues": 80, "clamped_motif_residues": 20, "rotation_det_r": 1.0, "gen1_hardcoded_rmsd_error_angstrom": 14.633, "unguarded_improper_rmsd_angstrom": 0.6124, "native_motif_rmsd_angstrom": 9.8258, "scipy_motif_rmsd_angstrom": 9.8258, "abs_diff_motif_rmsd": 0.0, "native_backbone_rmsd_angstrom": 15.523, "scipy_backbone_rmsd_angstrom": 15.523, "abs_diff_backbone_rmsd": 0.0, "native_tm_score": 0.167, "scipy_tm_score": 0.167, "abs_diff_tm_score": 0.0, "regime_classification": "0-Beaker Chiral Mirror-Image Reflection Rejected by det(R)=+1 Guard (RMSD = 15.52 A vs. unguarded 0.61 A, TM = 0.1670)", "concordant_with_scipy": true, "native_runtime_ms": 0.0433, "scipy_runtime_ms": 13.8607 } ], "ascii_summary_table": "========================================================================================================================================================\n TOOL BENCHMARK #22: Native Kabsch SO(3) Superposition, Active-Site Motif RMSD & TM-Score vs. Live SciPy v1.18.1 (linalg.svd)\n========================================================================================================================================================\nCohort Split PDB NRes Motif det(R) NatMotifA SciMotifA NatBB_A SciBB_A |ΔRMSD| Nat_TM Sci_TM |ΔTM| Match\n--------------------------------------------------------------------------------------------------------------------------------------------------------\nDEV-01 Development 1UYD 80 20 1.00 0.3355 0.3355 0.7846 0.7846 0.0000 0.9441 0.9441 0.0000 YES (100%)\nDEV-02 Development 6X3P 80 20 1.00 0.4250 0.4250 0.9183 0.9183 0.0000 0.9256 0.9256 0.0000 YES (100%)\nDEV-03 Development 1RX2 80 20 1.00 0.2674 0.2674 0.7086 0.7086 0.0000 0.9538 0.9538 0.0000 YES (100%)\nDEV-04 Development 4ZAM 80 20 1.00 0.4025 0.4025 0.8328 0.8328 0.0000 0.9376 0.9376 0.0000 YES (100%)\nDEV-05 Development 5RGF 80 20 1.00 0.2922 0.2922 0.6129 0.6129 0.0000 0.9648 0.9648 0.0000 YES (100%)\nDEV-06 Development 1ORC 60 20 1.00 36.8432 36.8432 39.6791 39.6791 0.0000 0.0077 0.0077 0.0000 YES (100%)\nRES-01 Reserve 4BDF 80 20 1.00 0.3580 0.3580 0.7997 0.7997 0.0000 0.9421 0.9421 0.0000 YES (100%)\nRES-02 Reserve 1G50 80 20 1.00 0.3465 0.3465 0.7176 0.7176 0.0000 0.9527 0.9527 0.0000 YES (100%)\nRES-03 Reserve 4URL 80 20 1.00 0.3719 0.3719 0.9015 0.9015 0.0000 0.9281 0.9281 0.0000 YES (100%)\nRES-04 Reserve 1ORC 64 20 1.00 0.3103 0.3103 0.6197 0.6197 0.0000 0.9524 0.9524 0.0000 YES (100%)\nRES-05 Reserve 1XAV 40 15 1.00 0.3155 0.3155 0.7503 0.7503 0.0000 0.8656 0.8656 0.0000 YES (100%)\nRES-06 Reserve 5RGF 80 20 1.00 9.8258 9.8258 15.5230 15.5230 0.0000 0.1670 0.1670 0.0000 YES (100%)\n--------------------------------------------------------------------------------------------------------------------------------------------------------\n" }