{ "run_date": "2026-09-20", "n_queries": 479, "n_covered": 117, "n_absent": 362, "n_panel_mapping_unresolved": 407, "recalls": [ { "k": 1, "hits": 7, "covered_percent": 5.982905982905983, "all_percent": 1.4613778705636744 }, { "k": 5, "hits": 15, "covered_percent": 12.820512820512821, "all_percent": 3.1315240083507305 }, { "k": 10, "hits": 19, "covered_percent": 16.23931623931624, "all_percent": 3.9665970772442587 }, { "k": 20, "hits": 28, "covered_percent": 23.931623931623932, "all_percent": 5.845511482254698 }, { "k": 50, "hits": 36, "covered_percent": 30.76923076923077, "all_percent": 7.515657620041754 } ], "subsets": { "confirmed_single_source_covered": { "n": 16, "hit_at_1": 1, "hit_at_5": 3, "hit_at_10": 4, "hit_at_20": 7, "R@1": 0.0625, "R@5": 0.1875, "R@10": 0.25, "R@20": 0.4375, "MRR": 0.1125717224659821, "median_rank": 178.0, "hit_at_50": 7, "R@50": 0.4375 }, "source_mapped_or_multiple_depicted_covered": { "n": 19, "hit_at_1": 1, "hit_at_5": 3, "hit_at_10": 4, "hit_at_20": 7, "R@1": 0.05263157894736842, "R@5": 0.15789473684210525, "R@10": 0.21052631578947367, "R@20": 0.3684210526315789, "MRR": 0.09491794569140503, "median_rank": 532.0, "hit_at_50": 7, "R@50": 0.3684210526315789 }, "all_candidate_covered_exploratory": { "n": 117, "hit_at_1": 7, "hit_at_5": 15, "hit_at_10": 19, "hit_at_20": 28, "R@1": 0.05982905982905983, "R@5": 0.1282051282051282, "R@10": 0.1623931623931624, "R@20": 0.23931623931623933, "MRR": 0.09300611328993882, "median_rank": 272.0, "hit_at_50": 36, "R@50": 0.3076923076923077 }, "all_queries_candidate_hits_including_absent": { "n": 479, "hit_at_1": 7, "hit_at_5": 15, "hit_at_10": 19, "hit_at_20": 28, "R@1": 0.014613778705636743, "R@5": 0.031315240083507306, "R@10": 0.03966597077244259, "R@20": 0.05845511482254697, "MRR": 0.022717568381884847, "median_rank": 272.0, "hit_at_50": 36, "R@50": 0.07515657620041753 }, "new_crops_candidate_covered_exploratory": { "n": 97, "hit_at_1": 6, "hit_at_5": 12, "hit_at_10": 15, "hit_at_20": 21, "R@1": 0.061855670103092786, "R@5": 0.12371134020618557, "R@10": 0.15463917525773196, "R@20": 0.21649484536082475, "MRR": 0.09356686553883188, "median_rank": 247.0, "hit_at_50": 29, "R@50": 0.29896907216494845 }, "previous_crops_candidate_covered": { "n": 20, "hit_at_1": 1, "hit_at_5": 3, "hit_at_10": 4, "hit_at_20": 7, "R@1": 0.05, "R@5": 0.15, "R@10": 0.2, "R@20": 0.35, "MRR": 0.09028646488280732, "median_rank": 484.5, "hit_at_50": 7, "R@50": 0.35 } }, "provenance": { "model": "DINOv2-L ft_b", "checkpoint_sha256": "c3ea295708f3747c696520abcc848c2fbbdc7eed4c42c32dd657d11f61e60db4", "index_sha256": "3fd09639ff615fbc3bd8e74f3d475f4923d197b46783f46eb863667a4c5b32cd", "query_manifest_sha256": "322022be1b6d2bb8a3f62c9ed36d20f98c8e899137b675f5258ac779f28586c1", "query_count": 479, "n_gallery_images": 836399, "n_gallery_entries": 38833, "score": "exact cosine, mean of top five reference-image similarities per PDB", "tie_policy": "descending score then alphabetical PDB ID", "preprocessing": { "size": [ 224, 224 ], "resize": "PIL bilinear (matches stage-B T.Resize)", "center_crop": false, "query_augmentation": false, "mean": [ 0.485, 0.456, 0.406 ], "std": [ 0.229, 0.224, 0.225 ] }, "new_encoder_inference": true, "training_performed": false, "score_rule_tuned_on_this_set": false, "script_sha256": "8659875200d4b222681e9d97d14bfd4f95cac4f8eeda03367dd194591e2e80fb", "server_code_sha256": "9054b81797f65270c188733e31f2e5172fd183a8383402a43003a1f7112f3a98", "aggregation_code_sha256": "33ac49fc1afbb4418851272c345ad2c7b1c2b085790ae2ff1b968d69abf68629", "report_code_sha256": "9d56cbcd0a822c0df1b9e362096360ef72b1d783905a0bed2199ffee9dda56d6", "splits_sha256": "d82370c65b7e23b2ca0ac3a4417e650edc25819fc7a1d5a2b5e57a991a8e86cd", "python": "3.11.16", "torch": "2.11.0+cu128", "numpy": "2.4.6", "gpu": "NVIDIA RTX A6000", "created_at": "2026-09-20T11:13:36Z", "scope": "All user-approved crops, including RNA-only diagnostic. Existing mapping certainty retained. Development diagnostic; embedded labels retained." }, "predictions_sha256": "5bfca2d8a4d21e1d7e3385a11c196a7b280c7aedb00a8d885c61ffb3529d646b", "interpretation": "Crop approval is not PDB mapping confirmation. Candidate-hit metrics accept any listed source accession and can be optimistic. Missing targets cannot be exact-ID successes. RNA is scored but excluded from protein mapped subsets. No structural grading or calibrated probabilities.", "selection": "Five top-10 candidate hits and three failures selected after inspecting results; illustrative, not a random or representative sample.", "examples": [ { "crop_id": "007_human-microsomal-triglyceride-transfer-protein__a_human", "title": "Microsomal triglyceride transfer protein", "outcome": "success", "query_image": "/wild/q_007_human-microsomal-triglyceride-transfer-protein__a_human.png", "result_image": "/wild/g_6i7s_asm1_v03.jpg", "source_pdb_ids": [ "6I7S" ], "source_rank": 1, "match_note": null, "query_pdb_label": "6I7S", "mapping_status": "source_mapped", "source_coverage": [ { "pdb_id": "6I7S", "present": true, "rank": 1, "score": 0.9013827443122864, "corpus_split": "train" } ], "result": { "rank": 1, "pdb_id": "6I7S", "render_id": "6i7s_asm1_v03", "object_id": "6i7s_asm1", "view": 3, "corpus_split": "train" }, "paper_title": "A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein", "source_url": "https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008941", "authors": "Meredith H. Wilson, Sujith Rajan, Aidan Danoff, Richard J. White, Monica R. Hensley, Vanessa H. Quinlivan, Rosario Recacha, James H. Thierer, Frederick J. Tan, Elisabeth M. Busch-Nentwich, Lloyd Ruddock, M. Mahmood Hussain, Steven A. Farber", "year": "2020", "license": "Creative Commons Attribution (CC BY), as stated by the source article; retain author and source attribution.", "license_url": "https://creativecommons.org/licenses/by/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "016_lysime-ef1-endolysin__a_left", "title": "LysIME-EF1 endolysin", "outcome": "success", "query_image": "/wild/q_016_lysime-ef1-endolysin__a_left.png", "result_image": "/wild/g_6ist_au_v13.jpg", "source_pdb_ids": [ "6IST" ], "source_rank": 4, "match_note": null, "query_pdb_label": "6IST", "mapping_status": "source_mapped", "source_coverage": [ { "pdb_id": "6IST", "present": true, "rank": 4, "score": 0.8781991004943848, "corpus_split": "val" } ], "result": { "rank": 4, "pdb_id": "6IST", "render_id": "6ist_au_v13", "object_id": "6ist_au", "view": 13, "corpus_split": "val" }, "paper_title": "Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage", "source_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1008394", "authors": "Biao Zhou, Xiangkai Zhen, Huan Zhou, Feiyang Zhao, Chenpeng Fan, Vanja Perčulija, Yigang Tong, Zhiqiang Mi, Songying Ouyang", "year": "2020", "license": "Creative Commons Attribution (CC BY), as stated by the source article; retain author and source attribution.", "license_url": "https://creativecommons.org/licenses/by/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "113_streptococcus-pyogenes-cas9-sgrna-in-complex-w__primary", "title": "Cas9–sgRNA–AcrIIA26 complex", "outcome": "success", "query_image": "/wild/q_113_streptococcus-pyogenes-cas9-sgrna-in-complex-w__primary.png", "result_image": "/wild/g_9zq6_au_v03.jpg", "source_pdb_ids": [ "9ZQ6" ], "source_rank": 8, "match_note": null, "query_pdb_label": "9ZQ6", "mapping_status": "panel_candidates", "source_coverage": [ { "pdb_id": "9ZQ6", "present": true, "rank": 8, "score": 0.8635202646255493, "corpus_split": "train" } ], "result": { "rank": 8, "pdb_id": "9ZQ6", "render_id": "9zq6_au_v03", "object_id": "9zq6_au", "view": 3, "corpus_split": "train" }, "paper_title": "Structural basis for inhibition of SpyCas9 by the anti-CRISPR protein AcrIIA26", "source_url": "https://doi.org/10.1042/bcj20250364", "authors": "Zheng I, Learn B, Bailey S.", "year": "2026", "license": "CC BY 4.0", "license_url": "https://creativecommons.org/licenses/by/4.0/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "059_porphyromonas-gingivalis-type-ix-secretion-sys__primary", "title": "PorE C-terminal domain", "outcome": "success", "query_image": "/wild/q_059_porphyromonas-gingivalis-type-ix-secretion-sys__primary.png", "result_image": "/wild/g_6top_asm1_v15.jpg", "source_pdb_ids": [ "6TOP" ], "source_rank": 4, "match_note": null, "query_pdb_label": "6TOP", "mapping_status": "panel_candidates", "source_coverage": [ { "pdb_id": "6TOP", "present": true, "rank": 4, "score": 0.7847325205802917, "corpus_split": "train" } ], "result": { "rank": 4, "pdb_id": "6TOP", "render_id": "6top_asm1_v15", "object_id": "6top_asm1", "view": 15, "corpus_split": "train" }, "paper_title": "Crystal structure of Type IX secretion system PorE C-terminal domain from Porphyromonas gingivalis in complex with a peptidoglycan fragment.", "source_url": "https://doi.org/10.1038/s41598-020-64115-z", "authors": "Trinh NTT, Tran HQ, Van Dong Q, Cambillau C, Roussel A, Leone P.", "year": "2020", "license": "CC BY 4.0", "license_url": "https://creativecommons.org/licenses/by/4.0/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "318_human-na-k-cl-cotransporter-nkcc1-pnkcc1-in-co__primary", "title": "Human NKCC1 cotransporter", "outcome": "success", "query_image": "/wild/q_318_human-na-k-cl-cotransporter-nkcc1-pnkcc1-in-co__primary.png", "result_image": "/wild/g_9c0h_au_v06.jpg", "source_pdb_ids": [ "9C0E", "9C0G", "9C0H" ], "source_rank": 1, "match_note": "Furosemide-bound 9C0E is absent. Retrieved 9C0H is NKCC1 with bumetanide: the same protein, a different drug-bound structure. A candidate hit, not an exact panel match.", "query_pdb_label": "9C0E", "mapping_status": "panel_candidates", "source_coverage": [ { "pdb_id": "9C0E", "present": false, "rank": null, "score": null, "corpus_split": "absent" }, { "pdb_id": "9C0G", "present": false, "rank": null, "score": null, "corpus_split": "absent" }, { "pdb_id": "9C0H", "present": true, "rank": 1, "score": 0.9049217104911804, "corpus_split": "train" } ], "result": { "rank": 1, "pdb_id": "9C0H", "render_id": "9c0h_au_v06", "object_id": "9c0h_au", "view": 6, "corpus_split": "train" }, "paper_title": "Structural basis for human NKCC1 inhibition by loop diuretic drugs", "source_url": "https://doi.org/10.1038/s44318-025-00368-6", "authors": "Zhao Y, Vidossich P, Forbush B, Ma J, Rinehart J, De Vivo M, Cao E.", "year": "2025", "license": "CC BY 4.0", "license_url": "https://creativecommons.org/licenses/by/4.0/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "001_erb1-beta-propeller__b", "title": "Erb1 beta-propeller", "outcome": "ranking_failure", "query_image": "/wild/q_001_erb1-beta-propeller__b.png", "result_image": "/wild/g_4zox_au_v13.jpg", "source_pdb_ids": [ "4U7A" ], "source_rank": 183, "match_note": null, "query_pdb_label": "4U7A", "mapping_status": "source_mapped", "source_coverage": [ { "pdb_id": "4U7A", "present": true, "rank": 183, "score": 0.8084653615951538, "corpus_split": "val" } ], "result": { "rank": 1, "pdb_id": "4ZOX", "render_id": "4zox_au_v13", "object_id": "4zox_au", "view": 13, "corpus_split": "train" }, "paper_title": "The Carboxy-Terminal Domain of Erb1 Is a Seven-Bladed ß-Propeller that Binds RNA", "source_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123463", "authors": "Wegrecki Marcin, Jose Luis Neira, Jeronimo Bravo", "year": "2015", "license": "Creative Commons Attribution (CC BY), as stated by the source article; retain author and source attribution.", "license_url": "https://creativecommons.org/licenses/by/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "039_cecr-a-tetr-family-transcriptional-regulator-t__primary", "title": "CecR transcriptional regulator", "outcome": "ranking_failure", "query_image": "/wild/q_039_cecr-a-tetr-family-transcriptional-regulator-t__primary.png", "result_image": "/wild/g_1sgm_au_v15.jpg", "source_pdb_ids": [ "9I1X" ], "source_rank": 63, "match_note": null, "query_pdb_label": "9I1X", "mapping_status": "panel_candidates", "source_coverage": [ { "pdb_id": "9I1X", "present": true, "rank": 63, "score": 0.8376396298408508, "corpus_split": "test" } ], "result": { "rank": 1, "pdb_id": "1SGM", "render_id": "1sgm_au_v15", "object_id": "1sgm_au", "view": 15, "corpus_split": "train" }, "paper_title": "Molecular basis of antibiotic sensing by the TetR family regulator CecR - a structural perspective.", "source_url": "https://doi.org/10.1111/febs.70318", "authors": "Pietrzyk-Brzezinska AJ, Koczurowska A, Orlikowska M, Nielipinski M, Nielipinska D, Sekula B.", "year": "2026", "license": "https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.", "license_url": "https://creativecommons.org/licenses/by/4.0/", "image_changes": "Cropped and resized from the source figure." }, { "crop_id": "005_glmm-phosphoglucosamine-mutase__left", "title": "GlmM phosphoglucosamine mutase", "outcome": "coverage_failure", "query_image": "/wild/q_005_glmm-phosphoglucosamine-mutase__left.png", "result_image": "/wild/g_3io1_au_v15.jpg", "source_pdb_ids": [ "6GYZ" ], "source_rank": null, "match_note": null, "query_pdb_label": "6GYZ", "mapping_status": "source_mapped", "source_coverage": [ { "pdb_id": "6GYZ", "present": false, "rank": null, "score": null, "corpus_split": "absent" } ], "result": { "rank": 1, "pdb_id": "3IO1", "render_id": "3io1_au_v15", "object_id": "3io1_au", "view": 15, "corpus_split": "train" }, "paper_title": "Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM", "source_url": "https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007537", "authors": "Tommaso Tosi, Fumiya Hoshiga, Charlotte Millership, Rahul Singh, Charles Eldrid, Delphine Patin, Dominique Mengin-Lecreulx, Konstantinos Thalassinos, Paul Freemont, Angelika Gründling", "year": "2019", "license": "Creative Commons Attribution (CC BY), as stated by the source article; retain author and source attribution.", "license_url": "https://creativecommons.org/licenses/by/", "image_changes": "Cropped and resized from the source figure." } ] }