Protpardelle-1c (cc94)

Overview

Author-evaluated generation configuration; checkpoint/version and sampling parameters remain those described in Appendix B.2.

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Evaluations and results

1 evaluation · 5 metric rows. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Protpardelle-1c (cc94)	Protocol: Genie 3 short monomer generation designability: Unconditional short monomer Designability Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.97 designability reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Protpardelle-1c (cc94) on Genie 3 short monomer generation designability: Unconditional short monomer Designability Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 10 (Protpardelle-1c (cc94)), column Designability
Configuration: Protpardelle-1c (cc94)	Protocol: Genie 3 short monomer generation diversity-tm-05: Unconditional short monomer Diversity, TM < 0.5 Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.13 diversity_tm_05 reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Protpardelle-1c (cc94) on Genie 3 short monomer generation diversity-tm-05: Unconditional short monomer Diversity, TM < 0.5 Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 10 (Protpardelle-1c (cc94)), column Diversity, TM < 0.5
Configuration: Protpardelle-1c (cc94)	Protocol: Genie 3 short monomer generation diversity-tm-06: Unconditional short monomer Diversity, TM < 0.6 Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.34 diversity_tm_06 reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Protpardelle-1c (cc94) on Genie 3 short monomer generation diversity-tm-06: Unconditional short monomer Diversity, TM < 0.6 Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 10 (Protpardelle-1c (cc94)), column Diversity, TM < 0.6
Configuration: Protpardelle-1c (cc94)	Protocol: Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.28 novelty_afdb reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Protpardelle-1c (cc94) on Genie 3 short monomer generation novelty-afdb: Unconditional short monomer Novelty, AFDB Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 10 (Protpardelle-1c (cc94)), column Novelty, AFDB
Configuration: Protpardelle-1c (cc94)	Protocol: Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB Dataset subset: 500 generated monomers per run; lengths 50–250 in steps of 50; three runs (Genie 3 short monomer generation split)	0.28 novelty_pdb reported score · higher Uncertainty: Not reported Coverage: generated per run: 500; repeats: 3; note: Three repeated runs; metric-specific valid subsets not assigned a pooled denominator.	Author-reported evaluation · source checked Methods, coverage and source Protpardelle-1c (cc94) on Genie 3 short monomer generation novelty-pdb: Unconditional short monomer Novelty, PDB Unconditional short monomer generation: 100 structures at each length 50, 100, 150, 200 and 250 (500 samples per run); 3 repeated runs; Table 3 reports the authors’ average across runs. Designability uses minimum C-alpha scRMSD <2 angstrom across 8 ProteinMPNN sequences refolded with ESMFold. Diversity and novelty use FoldSeek release 10 (2025-01-19); exact definitions and reference sets in Appendix B.1. Method-specific checkpoints and sampling settings remain as Appendix B.2. Aggregation: Mean over three repeated runs Genie 3 primary paper v1, Table 3 · PDF page 20, Appendix B.3, Table 3, data row 10 (Protpardelle-1c (cc94)), column Novelty, PDB

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