{"meta":{"snapshot":"2026-10-09","title":"Figure 2 packet with audited catalog additions","paper_rows":2488,"catalog_rows":764,"catalog_snapshot":"2026-10-09T18:44:57.859825+00:00","conditioning_rows":665,"conditioning_snapshot":"2026-10-09T19:33:16.958042+00:00","source_rows":3252,"unique_cohorts":2251,"source_revision":"e3d59cde0c310c97ebc7e25af0158bd2b0a01365","live_database":false,"archive":"s3://archive-e04a/benchmarks/supplement-20261009/supplement-20261009.tar.gz","files":{"paper_source_data.csv":{"sha256":"5f71454272467ea86a5ef0f4ad8a7c781ca31eff8d57497e83c87aa8820cc34b"},"METHODS.md":{"sha256":"e0df1aa21f774ae13450e128293f5a45ea2e0b9214a4c5bfcefe4caa4a3c7442"},"SOURCE_NOTES.md":{"sha256":"21063bf7014f2d43e945a00185943d067c8941afd5d935c055e1f04aead2751a"},"catalog_additions.json":{"sha256":"30937fcedd0c28263184e20ac6f62cd0dfd5718b3f1b773ddf3392b82b291316"},"conditioning_additions.json":{"sha256":"7c2bd7e961dc86d476b9d6dbd18805b7f5cb78f3eb8c8591856ac28d1c48acbc"},"rfd4_ppi_timing.json":{"sha256":"69c4fc14a8f089dbc3b42aae9184639fbadfdc53a355595da9c3f02210f78956"},"source_data.csv":{"sha256":"7bcf5c73197505cdeb885f490ad3a1324c8af9491c33de7c0df5ff7603ae8a8c"}},"rfd4_ppi_timing_refreshed_at":"2026-10-09T20:41:02.319317+00:00"},"models":{"alphaprotein_novo":{"name":"AlphaProtein-novo \u00b7 Codesign","color":"#32B39B","family":"generative","method":{"text":"Native 1000-step joint codesign. Paired LigandMPNN arm uses one sequence at 0.1, checkpoint 030, atom context on, sidechain context off, no packing. CPU MPNN adds zero GPU seconds; shared scaffold generation time is inherited, not omitted. Native APN1 composite-ligand handling of M0110 changes interface interpretation and is disclosed.","reference_label":"AlphaProtein-novo","reference_url":"https://github.com/google-deepmind/alphaprotein-novo"}},"alphaprotein_novo_ligandmpnn":{"name":"AlphaProtein-novo \u00b7 LigandMPNN","color":"#8D52AD","family":"generative","method":{"text":"Native 1000-step joint codesign. Paired LigandMPNN arm uses one sequence at 0.1, checkpoint 030, atom context on, sidechain context off, no packing. CPU MPNN adds zero GPU seconds; shared scaffold generation time is inherited, not omitted. Native APN1 composite-ligand handling of M0110 changes interface interpretation and is disclosed.","reference_label":"AlphaProtein-novo","reference_url":"https://github.com/google-deepmind/alphaprotein-novo"}},"bindcraft":{"name":"BindCraft","color":"#B94B47","family":"hallucination","method":{"text":"One 75/45/5/15 optimization trajectory, then one soluble ProteinMPNN v_48_020 sequence at 0.1. Three continuation gates bypassed to retain bad trajectories. No post-MPNN fold/relax/filter/rank. Native independent batch 1; exact lengths warmed. Native interface-fixed residues retained. Output sidechains incompatible with the new sequence become unobserved rather than being grafted.","reference_label":"BindCraft tutorial","reference_url":"https://github.com/martinpacesa/BindCraft/wiki/De-novo-binder-design-with-BindCraft"},"protocol_methods":{"native_pipeline":{"text":"Native optimization with continuation gates and beta adaptation, relaxation, up to 20 soluble ProteinMPNN proposals and native AF2 validation; stops after at most two accepted candidates. One original designates the retained candidate with highest native Average_i_pTM regardless of native filter acceptance, using its highest-pLDDT validation model. If none remains, retain the saved trajectory. All intrinsic proposals and validations are charged. No restart to replace a rejected original. Batch size 1; separately warmed exact-length signatures. Common AF3 evaluates the designated output only.","reference_label":"BindCraft repository","reference_url":"https://github.com/martinpacesa/BindCraft"}}},"bindcraft2":{"name":"BindCraft2","color":"#C7782D","family":"hallucination","method":{"text":"One 50/25/45/5/15 trajectory, then one native soluble-MPNN redesign at 0.1. Continuation gates disabled; no independent validation or relaxation. Native independent batch 1, unchunked; resident AF2/MPNN pair, separately warmed signatures. Preserve exact native redesign constraints and report omitted incompatible sidechains.","reference_label":"BindCraft2","reference_url":"https://github.com/PacesaLab/BindCraft2"},"protocol_methods":{"native_pipeline":{"text":"Native optimization with continuation gates, ten distinct MPNN candidates, three-recycle validation and early stop after three passing candidates. One original designates the highest native i_pDAE retained candidate regardless of native filter acceptance, or the saved trajectory if none is available. Native relaxation is disabled by default. Batch size 1, resident models, exact-length warmup; candidate history is reset per original. Intrinsic validation and selection are included in generation time, separately from common AF3.","reference_label":"BindCraft2 repository","reference_url":"https://github.com/PacesaLab/BindCraft2"}}},"boltzgen":{"name":"BoltzGen","color":"#32B39B","family":"generative","method":{"text":"Design: 500 steps/3 recycles; inverse folding: 200 steps/3 recycles, one final sequence. Original indices 0\u201399 use diverse, 100\u2013199 adherence, preserving the native quarter settings across shards. No terminal folding/filtering/ranking. Atom hotspots become residue hotspots; PPI is all-atom. Seven heme cases use disclosed native bond-type projections; difficult chemistry uses source-derived archives, never author benchmark molecules.","reference_label":"BoltzGen","reference_url":"https://github.com/HannesStark/boltzgen"}},"disco":{"name":"DISCO","color":"#4A9463","family":"generative","method":{"text":"Native diverse/max joint draw, 200 diffusion steps/four recycles. No extra sequence designer. SDF/JSON derives from shared CIF chemistry, never checked-in benchmark SDFs. Same-target/exact-length batches; all batch members retained. Native hydrogen/bond-order losses are documented, not repaired.","reference_label":"DISCO","reference_url":"https://github.com/DISCO-design/DISCO"}},"esmfold2":{"name":"ESMFold2","color":"#463D73","family":"hallucination","method":{"text":"150 inversion steps, two pinned models/four intrinsic hero critics. Critic 0 is predesignated; no common-AF3 ranking. Target sequence/residue hotspots, not target coordinates. Multichain extension preserves all target copies and native whole-complex ipTM, including target\u2013target contributions. Intrinsic critics are not separate benchmark attempts.","reference_label":"ESM binder-design tutorial","reference_url":"https://github.com/Biohub/esm/blob/main/cookbook/tutorials/binder_design.ipynb"}},"genie3":{"name":"Genie3","color":"#C4963B","family":"generative","method":{"text":"One 100-step generative draw and one CA-MPNN sequence at 0.1. No search or ColabFold. Force the original hotspot, using target CA and source hotspot sidechain geometry, not extended contacts. Native CA-only outputs stay CA-only and are evaluated with binder CA RMSD. Some executed input receipts reference an earlier source release; exact executed files remain preserved, not silently rebound to a newer queue.","reference_label":"Genie3","reference_url":"https://github.com/aqlaboratory/genie3"},"protocol_methods":{"native_pipeline":{"text":"Separate search pipeline: 100 diffusion steps, beam width 4, scoring every 25 steps; 64 internal candidate evaluations per original. Each candidate gets one CA-MPNN sequence at temperature 0.1 and ColabFold AF2-Multimer v3, one model/three recycles with target templating. Select the global maximum negative mean interface PAE; publish its generated CA backbone, not the AF2-refolded backbone. Preserve original hotspot sidechains; no extended conditioning. Independent original batch size 1. Diffusion, MPNN and internal folding/search are all charged. The catalog currently uses an approved timing estimate: one padding-optimized measured replicate per target extrapolated to 200 originals. Common AF3 is additional and separately timed.","reference_label":"Genie3 repository","reference_url":"https://github.com/aqlaboratory/genie3"}}},"odesign":{"name":"ODesign","color":"#B798CD","family":"generative","method":{"text":"Native scaffold generation followed by the corrected one-LigandMPNN0.1, source-mask-fixed sequence route. No terminal AF3 selection. Native AME receives disclosed extra observed motif context and is not a strict tip-only baseline. Fixed-ligand and fixed-DNA membership is labeled explicitly. Original-generation timing is a proxy, as described above.","reference_label":"ODesign","reference_url":"https://github.com/OTeam-AI4S/ODesign"}},"pipelines":{"name":"RFdiffusion3","color":"#186C70","family":"generative","method":{"text":"Native 200 steps, CFG off, step size 1.5; one LigandMPNN sequence at temperature 0.1, no downstream pipeline screening. DNA uses the DNA-finetuned checkpoint. Native JSON/derivatives preserve shared lengths and correspondence. Approved PPI OXT omission and native M0110 bond/charge/preprocessing losses are retained. Ligands can follow native reference conformers; no stereo repair.","reference_label":"Foundry","reference_url":"https://github.com/RosettaCommons/foundry"}},"protein_hunter":{"name":"Protein-Hunter","color":"#8B969D","family":"refinement","method":{"text":"Seven approved native refinement cycles, 100%-X initialization, 200 steps/3 recycles, MPNN 0.1. SolubleMPNN for PPI; LigandMPNN for ligands/DNA. Retain highest native ipTM cycle among those with \u226420% alanine. All intrinsic cycles are timed. Native rejection and writer/chemistry defects are not rescued. PPI guidance is residue hotspots and CA/CB/frame guidance, not hard sidechain enforcement.","reference_label":"Protein-Hunter","reference_url":"https://github.com/yehlincho/Protein-Hunter"}},"proteina_complexa":{"name":"Proteina-Complexa","color":"#8D52AD","family":"generative","method":{"text":"One 400-step joint draw, no additional MPNN/selection. PPI uses V1; AME V2/LoRA32; fixed small molecules use the corrected dedicated V1/LoRA32 ligand route. Native matcher is retained: unmatched motifs fail downstream. PPI and ligand inputs use native atom37/template features and residue-projected hotspots. No DNA or fully unfixed ligand route.","reference_label":"Proteina-Complexa","reference_url":"https://github.com/NVIDIA-BioNeMo/Proteina-Complexa"}},"rfd4-search-multimer":{"name":"RFD4-Proteina \u00b7 Search","color":"#243858","family":"generative","method":{"text":"Joint sequence/structure generation with stored Low/Medium/High schedules; exact schedule/checkpoint comes from each native config. Search is a separate intrinsic workflow: AF2-Multimer for PPI and OF3 for the other benchmarks, with all search work timed. Preserve native motif correspondence; unmatched required motifs fail. Historical PPI-AA validation is explicitly separate from the newer BB campaign.","reference_label":"RFD4 repository","reference_url":"https://github.com/RosettaCommons/RFD4-Proteina"}},"rfd4_proteina_high":{"name":"RFD4-Proteina \u00b7 High","color":"#3B5A8D","family":"generative","method":{"text":"Joint sequence/structure generation with stored Low/Medium/High schedules; exact schedule/checkpoint comes from each native config. Search is a separate intrinsic workflow: AF2-Multimer for PPI and OF3 for the other benchmarks, with all search work timed. Preserve native motif correspondence; unmatched required motifs fail. Historical PPI-AA validation is explicitly separate from the newer BB campaign.","reference_label":"RFD4 repository","reference_url":"https://github.com/RosettaCommons/RFD4-Proteina"}},"rfd4_proteina_high_search":{"name":"RFD4-Proteina \u00b7 Search","color":"#243858","family":"generative","method":{"text":"Joint sequence/structure generation with stored Low/Medium/High schedules; exact schedule/checkpoint comes from each native config. Search is a separate intrinsic workflow: AF2-Multimer for PPI and OF3 for the other benchmarks, with all search work timed. Preserve native motif correspondence; unmatched required motifs fail. Historical PPI-AA validation is explicitly separate from the newer BB campaign.","reference_label":"RFD4 repository","reference_url":"https://github.com/RosettaCommons/RFD4-Proteina"}},"rfd4_proteina_low":{"name":"RFD4-Proteina \u00b7 Low","color":"#7297C6","family":"generative","method":{"text":"Joint sequence/structure generation with stored Low/Medium/High schedules; exact schedule/checkpoint comes from each native config. Search is a separate intrinsic workflow: AF2-Multimer for PPI and OF3 for the other benchmarks, with all search work timed. Preserve native motif correspondence; unmatched required motifs fail. Historical PPI-AA validation is explicitly separate from the newer BB campaign.","reference_label":"RFD4 repository","reference_url":"https://github.com/RosettaCommons/RFD4-Proteina"}},"rfd4_proteina_medium":{"name":"RFD4-Proteina \u00b7 Medium","color":"#416FA9","family":"generative","method":{"text":"Joint sequence/structure generation with stored Low/Medium/High schedules; exact schedule/checkpoint comes from each native config. Search is a separate intrinsic workflow: AF2-Multimer for PPI and OF3 for the other benchmarks, with all search work timed. Preserve native motif correspondence; unmatched required motifs fail. Historical PPI-AA validation is explicitly separate from the newer BB campaign.","reference_label":"RFD4 repository","reference_url":"https://github.com/RosettaCommons/RFD4-Proteina"}},"rfdiffusion":{"name":"RFdiffusion","color":"#667078","family":"generative","method":{"text":"50-step Complex_base draw with example CA/frame noise scales 0; one ProteinMPNN v_48_020 sequence at 0.1. Resident native batch 1. No Rosetta/refold/selection. Explicit contig/chain maps retain target copies and gaps. Preserve native backbone-only output and atom omissions.","reference_label":"RFdiffusion binder design","reference_url":"https://github.com/RosettaCommons/RFdiffusion#binder-design"}},"rfdiffusion2":{"name":"RFdiffusion2","color":"#C4963B","family":"generative","method":{"text":"AME RFD_140 checkpoint, 100 native flow steps, one LigandMPNN 0.1 sequence with native packing/context. Resident native batch 1. M0110 uses the explicitly approved disconnected ligand projection: preserve source atoms/coordinates but omit two bonds in the native derivative. This is not equivalent physical topology. Native guidepost matching/idealization is retained.","reference_label":"RFdiffusion2","reference_url":"https://github.com/RosettaCommons/RFdiffusion2"}},"halludesign":{"name":"HalluDesign","color":"#A36085","family":"refinement","method":{"text":"Native Protenix refinement pipeline: 10 cycles, 150 refinement steps, two MPNN proposals and five ranked predictions; Protenix model_beta1_v0.2.0.pt with 10 model recycles/200 prediction steps. PPI enables interaction optimization and selection from cycle 0. DNA starts from the shared unfixed target sequences and uses the 120\u2013150-residue binder queue. Target sequences are retained, not hard target-coordinate templates. Final cycle skips coordinate refinement; designate its first native eval_plddt-ranked packed structure with its MPNN sequence. No common-AF3 selection or acceptance restarts. Native batch size 1; intrinsic MPNN/cofolding/selection is generation compute.","reference_label":"HalluDesign repository","reference_url":"https://github.com/MinchaoFang/HalluDesign"},"protocol_methods":{"native_pipeline":{"text":"Native Protenix refinement pipeline: 10 cycles, 150 refinement steps, two MPNN proposals and five ranked predictions; Protenix model_beta1_v0.2.0.pt with 10 model recycles/200 prediction steps. PPI enables interaction optimization and selection from cycle 0. DNA starts from the shared unfixed target sequences and uses the 120\u2013150-residue binder queue. Target sequences are retained, not hard target-coordinate templates. Final cycle skips coordinate refinement; designate its first native eval_plddt-ranked packed structure with its MPNN sequence. No common-AF3 selection or acceptance restarts. Native batch size 1; intrinsic MPNN/cofolding/selection is generation compute.","reference_label":"HalluDesign repository","reference_url":"https://github.com/MinchaoFang/HalluDesign"}}}},"labels":{"M0040_13pk":"M0040 13pk","M0050_1dbt":"M0050 1dbt","M0058_1cju":"M0058 1cju","M0078_1al6":"M0078 1al6","M0092_1dli":"M0092 1dli","M0093_1dqa":"M0093 1dqa","M0096_1chm":"M0096 1chm","M0097_1ctt":"M0097 1ctt","M0110_1c0p":"M0110 1c0p","M0129_1os7":"M0129 1os7","M0151_1q0n":"M0151 1q0n","M0157_1qh5":"M0157 1qh5","M0179_1q3s":"M0179 1q3s","M0188_1xel":"M0188 1xel","M0209_1lij":"M0209 1lij","M0255_1mg5":"M0255 1mg5","M0315_1ey3":"M0315 1ey3","M0349_1e3v":"M0349 1e3v","M0365_1pfk":"M0365 1pfk","M0375_4ts9":"M0375 4ts9","M0500_1e3i":"M0500 1e3i","M0552_1fgh":"M0552 1fgh","M0555_1f8r":"M0555 1f8r","M0584_1ldm":"M0584 1ldm","M0630_1j79":"M0630 1j79","M0636_1uaq":"M0636 1uaq","M0663_1rk2":"M0663 1rk2","M0664_2dhn":"M0664 2dhn","M0674_1uf7":"M0674 1uf7","M0710_1ra0":"M0710 1ra0","M0717_1x7d":"M0717 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ideal","N-acetyl-alpha-neuraminic_acid_final_0":"N-acetyl-alpha-neuraminic acid","NAD_final_0":"NAD","NDI_final_0":"NDI","Ni_ideal":"Ni ideal","PDI_final_0":"PDI","PFOA_final_0_PFOS_final_0_combined":"PFOA PFOS","PLP_final_0":"PLP","Rose_Bengal_final_0":"Rose Bengal","UV-328_final_0":"UV-328","Zn_ideal":"Zn ideal","acetyl_coenzyme_a_final_0":"acetyl coenzyme a","aflatoxin_B1_final_0":"aflatoxin B1","apixaban_final_0":"apixaban","benzo_a_pyrene_final_0":"benzo a pyrene","beta-d-mannopyranose_final_0":"beta-d-mannopyranose","bilirubin_final_0":"bilirubin","biotin_final_0":"biotin","caffeine_final_0":"caffeine","chloramphenicol_final_0":"chloramphenicol","cholesterol_final_0":"cholesterol","cholic_acid_final_0":"cholic acid","coenzyme_A_final_0":"coenzyme A","coenzyme_f420_final_0":"coenzyme f420","colchicine_final_0":"colchicine","digoxigenin_final_0":"digoxigenin","domoic_acid_final_0":"domoic acid","dopamine_final_0":"dopamine","erythromycin_a_final_0":"erythromycin 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