{"as_of":"2026-08-14T16:15:00Z","caps":{"database_statements":6,"inbound":100,"outbound":100},"context_digest":"sha256:baf6e2cd5fc9464bb68be761b2e3322db927987d750286426849991f77554af6","coverage":[{"denominator":99,"lane":"reference_resolution","note":"Typed states for the displayed outbound observations.","records_observed":99,"source":"paper_references, paper_reference_links","source_observed_at":"2026-05-14T22:11:30.437422Z","state":"measured"},{"denominator":101,"lane":"standing_notices","note":"One-hop event checks from named stored sources.","records_observed":101,"source":"scholarly_work_events, retraction_status_cache","source_observed_at":"2026-08-14T06:32:32.682623+00:00","state":"measured"},{"denominator":2,"lane":"inbound_itemization","note":"Pith citing papers itemized under the disclosed page cap.","records_observed":2,"source":"paper_references, paper_reference_links","source_observed_at":"2026-08-02T08:00:03.635400Z","state":"measured"},{"denominator":1,"lane":"external_citation_measurements","note":"A source-named dated measurement, never combined with another source.","records_observed":0,"source":"cited_works","source_observed_at":null,"state":"measured"}],"external_citation_measurements":[],"inbound":[{"citation":{"cited_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":null,"pith_arxiv_id":"2605.10978","snapshot_observed_at":"2026-07-13T06:39:26.167502Z","title":"arXiv preprint arXiv:2605.10978 , year=","venue":null,"work_id":null,"year":null},"citing_paper":{"arxiv_id":"2607.08803","last_updated":"2026-07-15T08:32:58Z","snapshot_observed_at":"2026-08-14T06:44:39.301384Z","submitted_at":"2026-07-09T06:56:39Z","title":"TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology","version":1},"reference_index":4,"source":"arxiv_source","source_observed_at":"2026-07-13T06:39:26.167502Z"},"links":{"cited_paper":"/paper/2605.10978","citing_paper":"/paper/2607.08803"},"observation_digest":"sha256:1afac180f828f33aeed5f4aaff9835c88eaa5d47515911f36cb6ec31139eedca","observation_id":"e03a5c91-9da5-4728-a0ed-3747abeef42c","resolution":{"observed_at":"2026-07-13T06:39:26.167502Z","resolver_source":null,"status":"unresolved"},"standing_notice":{"events":[],"reason":"canonical_work_link_unavailable","source_receipts":[],"state":"unavailable"}},{"citation":{"cited_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":null,"pith_arxiv_id":"2605.10978","snapshot_observed_at":"2026-08-02T08:00:03.635400Z","title":"arXiv preprint arXiv:2605.10978 , year=","venue":null,"work_id":null,"year":null},"citing_paper":{"arxiv_id":"2607.08803","last_updated":"2026-07-15T08:32:58Z","snapshot_observed_at":"2026-08-14T06:44:39.301384Z","submitted_at":"2026-07-09T06:56:39Z","title":"TheBioCollection: Unified Pre-Training Scale LLM Corpus for Biology","version":2},"reference_index":4,"source":"arxiv_source","source_observed_at":"2026-08-02T08:00:03.635400Z"},"links":{"cited_paper":"/paper/2605.10978","citing_paper":"/paper/2607.08803"},"observation_digest":"sha256:888ded8da315c6b3cc50cfeaccd734e702d81aa9ac4ee94296dbb77b66cda56d","observation_id":"f3bd4ecf-c646-4256-8a8b-7933232bc2cb","resolution":{"observed_at":"2026-08-02T08:00:03.635400Z","resolver_source":null,"status":"unresolved"},"standing_notice":{"events":[],"reason":"canonical_work_link_unavailable","source_receipts":[],"state":"unavailable"}}],"links":{"evidence":"/evidence","html":"/paper/2605.10978/citation-record","integrity":"/paper/2605.10978/integrity","json":"/paper/2605.10978/citation-record.json","paper":"/paper/2605.10978"},"outbound":[{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Computational protein design.Nature Reviews Methods Primers, 5(1):13","venue":null,"work_id":"f42fad6d-374f-4dbe-8707-4cb1490172f7","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":1,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:48010fcea0cf904a952f1f2a905cb47269b35265e5c787fa1c099d91f9ff6ded","observation_id":"f83076c2-4687-4d77-a970-c800a079cfa1","resolution":{"observed_at":"2026-05-14T22:48:14.840881Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Claude opus 4.6","venue":null,"work_id":"223ff2f8-0388-4580-8f66-d54f2c2d4b5f","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":2,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:20594afdd083e6283034a18ffea967597704e9c2d6b66d16c1f603b0b63153db","observation_id":"6e1e99fb-dd11-4084-acfb-52affc6ad4a4","resolution":{"observed_at":"2026-05-14T22:48:14.844541Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Miniprotein design: past, present, and prospects.Accounts of Chemical Research, 50(9):2085–2092","venue":null,"work_id":"33fd1752-8113-4ae5-97ee-0e1aed9239ec","year":2085},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":3,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:1381a74bdf60c2fa103f56214983f8f7c6dbe9108c2e207b01d2ef2c6e0987c5","observation_id":"ba8a6e8f-e339-475a-a47f-5bd96be56a06","resolution":{"observed_at":"2026-05-14T22:48:14.823774Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Atomically accurate de novo design of antibodies with rfdiffusion.Nature, 649(8095):183–193","venue":null,"work_id":"9af9bdc1-d9a5-4fbd-a8d3-81a7b5be95e5","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":4,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:09b7824d393aafcfe6680f0c3062d8e1dded079a11cdb9ad3caa353621a72c19","observation_id":"f8d1cfc0-af94-43d2-aa44-6d3e3f51bd99","resolution":{"observed_at":"2026-05-14T22:48:14.849122Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"The interpro protein families and domains database: 20 years on.Nucleic Acids Research, 49(D1):D344–D354","venue":null,"work_id":"7a29ffa0-14bb-48e2-b06e-c656d43ee7da","year":2021},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":5,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6463080c9f9ff5351ceca04788d86c9fd6e33ff46e0020378b5774158b47ef1e","observation_id":"e61e07a0-48d5-4f98-909c-bb84e6819314","resolution":{"observed_at":"2026-05-14T22:48:14.836738Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, et al","venue":null,"work_id":"78a21a2c-eac4-4148-93eb-3b5ba91f51de","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":6,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:e8e8beabc380d2e2b6554d1049d1c1d8e85b52dc5d323d98bbd83d28805b1818","observation_id":"558aebae-a327-4ac0-a733-37b402264598","resolution":{"observed_at":"2026-05-14T22:48:14.857198Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2402.13653","last_updated":"2024-11-18T19:32:06Z","snapshot_observed_at":"2026-08-13T04:59:11.641980Z","submitted_at":"2024-02-21T09:38:17Z","title":"PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models","version":2},"cited_work":{"arxiv_id":"2402.13653","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2402.13653","snapshot_observed_at":"2026-06-28T19:32:35.071768Z","title":"Pqa: Zero-shot protein question answering for free-form scientific enquiry with large language models","venue":null,"work_id":"38f428c0-e002-4b7f-a4a1-195a1dc32ae5","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":7,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2402.13653","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:2a960f71bfe0ba3027c6fcc2dc91017bd6c7836ac0969261927d9f473b60bf8f","observation_id":"8ada55ff-f85f-4c52-acdc-e17550213bc4","resolution":{"observed_at":"2026-05-14T22:13:04.898927Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-10T20:07:33.822136Z","title":"Pyrosetta: a script-based interface for implementing molecular modeling algorithms using rosetta.Bioinformatics, 26(5):689–691","venue":null,"work_id":"0d4b6644-ef9d-45ee-b62f-cac7d58ae49f","year":2010},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":8,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b0c4b771ceaf09ad0c97b036e0e48be80217d2726193d3fc933141afa4b45730","observation_id":"71256527-4b68-4b89-9b25-8afcd4c4bce9","resolution":{"observed_at":"2026-05-14T22:48:14.794844Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Cheng, R","venue":null,"work_id":"9ee5c6da-8819-4ff0-9425-086ffe8f087e","year":2014},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":9,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:9a86e2ae73e763e23d282c566eab8fda31a9fdcf7c003d86318640a7ec0fe6cf","observation_id":"3cd7ae0d-02a7-4c1d-80e5-564fcd28514e","resolution":{"observed_at":"2026-05-14T22:48:14.853221Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Stable de novo protein design via joint conformational landscape and sequence optimization","venue":null,"work_id":"31a95fc8-4b79-440e-b41b-ec7caa6bc29f","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":10,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:606decf043383387788b82d4c8e946fe6b2567c3a6c0d69416f4e1547b4a534a","observation_id":"39f21a54-de0d-4c78-9ab8-b8c13c251d86","resolution":{"observed_at":"2026-05-14T22:48:14.828293Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Sparks of function by de novo protein design","venue":null,"work_id":"49fbddbf-0047-4afc-820b-9b172a64e4a3","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":11,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:c622afc4bec7041f326c83c622cf47e71a0fd38e8c466dfaf923ddce39a3e6d8","observation_id":"9814f904-a94c-412b-b0f6-1d7c31f83a7c","resolution":{"observed_at":"2026-05-14T22:48:14.832441Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Rational protein design.Current Opinion in Structural Biology, 97:103224","venue":null,"work_id":"bd8cf632-5206-4894-ad31-a6efd1345f3e","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":12,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:06a4910ac4c1291f2249aaf392270bd8d6f6b6314dd18e910666f97246f8cf14","observation_id":"3b9ba505-10cc-4ae9-836f-e31c17d832fd","resolution":{"observed_at":"2026-05-14T22:48:14.799158Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Biopython: freely available python tools for computational molecular biology and bioinformatics.Bioinformatics, 25(11):1422–1423","venue":null,"work_id":"bced4930-7a70-40a9-adec-f026568a04a7","year":2009},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":13,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:3df0d02ea6cd9a140372768e9ae50ba559a5c64bf53e61c9f65bc715ef9f4c38","observation_id":"3978acdf-7f04-4bca-9bd1-a8024c39ecc9","resolution":{"observed_at":"2026-05-14T22:48:14.702524Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":null,"venue":null,"work_id":"32a8b062-90cf-4822-b50e-fe991fce7d1b","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":14,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b492f006da479583d934bf1a53c6bb3c4330263185ad61e2efd3dabe9454c23b","observation_id":"6e8fd057-de46-4800-ab0f-f36a0040682b","resolution":{"observed_at":"2026-05-14T22:48:14.642532Z","resolver_source":"raw_fallback","status":"unresolved"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Crowd- sourced protein design: Lessons from the adaptyv egfr binder competition.bioRxiv, pages 2025–04","venue":null,"work_id":"b4089de6-1634-462b-9b0f-3d2e56da779d","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":15,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:c10daa19aac45179314bb8fee653fc86104282c010eacdf71e24e418f052c358","observation_id":"4dc8b469-0d42-4a42-8645-381144e433d8","resolution":{"observed_at":"2026-05-14T22:48:14.636589Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"De novo protein design: fully automated sequence selection.Science, 278(5335):82–87","venue":null,"work_id":"24e06777-6112-4ab5-a7f8-02a6f6eed0a3","year":1997},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":16,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:ceb35762332aa6f3820571089928e5edde68d3eae3c76c486f4316326a91c4aa","observation_id":"ff07d580-7f17-4779-9eef-7d3c41fd69af","resolution":{"observed_at":"2026-05-14T22:48:14.547769Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Toward de novo protein design from natural language","venue":null,"work_id":"64a24ce4-55d2-4feb-9101-df24cb2cdc36","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":17,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:c8e858927b289058c4bfda11e1da71b488d3e2f086268fd5dd2d1bed0a267869","observation_id":"200fe115-2ed8-4639-99e7-2304be9ab325","resolution":{"observed_at":"2026-05-14T22:48:14.646693Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Robust deep learning–based protein sequence design using proteinmpnn.Science, 378(6615):49–56","venue":null,"work_id":"9d1f9b9b-d233-4d29-89f8-bee80d6020fc","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":18,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:bb97c0022e6003ba6dd7c1c6be7d8007e1c88fb1a5b57afcd92c9c3b1dd88a46","observation_id":"b82de2eb-3315-4769-896e-fba5b88c871e","resolution":{"observed_at":"2026-05-14T22:48:14.632465Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Atomic context-conditioned protein sequence design using ligandmpnn.Nature Methods, 22(4):717–723","venue":null,"work_id":"af029cfc-4a58-4722-bcb7-f51a989caf3c","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":19,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:d8cab2269c91453a3e63ac003bd0f994f7d73ffea956ef2c41ce94a670dfa984","observation_id":"43bc9a40-efc2-4d80-b833-aef6f5e94345","resolution":{"observed_at":"2026-05-14T22:48:14.774243Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Gemini 3.1 pro - model card","venue":null,"work_id":"ba2d4152-0154-4dc5-82ce-813f48a9be9f","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":20,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:3d93bb89a4ea41958964928307aa7267095f9806eec890872762033b5e135e92","observation_id":"67aa57b8-7dc8-4bf8-923e-4411c7ab1b7c","resolution":{"observed_at":"2026-05-14T22:48:14.748748Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Deepseek-v4: Towards highly efficient million-token context in- telligence","venue":null,"work_id":"a286853b-d42a-460e-90f3-f9dbbc50f7be","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":21,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:196de8dc7609f66431a1d3dcc9ea564237480c58758ce3996b13837265580b22","observation_id":"8b12d048-1e57-4bcd-ba4c-dddd2fcadf43","resolution":{"observed_at":"2026-05-14T22:48:14.757822Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-07T23:04:15.099819Z","title":"Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, and Karsten Kreis","venue":null,"work_id":"b7957e2b-7f9c-44c8-a8c3-d474b52550b0","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":22,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:9131c0a63596af1f552ab12912fcbc8930ab90dad88aa5b1eb8fb3add70fc87e","observation_id":"f274434b-4a1e-4d73-88ca-2fe904fcdc84","resolution":{"observed_at":"2026-05-14T22:48:14.739404Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Trans- fer learning to leverage larger datasets for improved prediction of protein stability changes","venue":null,"work_id":"aba18aa3-f5c6-417c-a02c-cde6c08d89a7","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":23,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b1a95176916bb87e0caa807f7f3bc852180317583121dcf065bfe43889bd5493","observation_id":"6f841fef-7e45-4799-b1f8-ca46e134526f","resolution":{"observed_at":"2026-05-14T22:48:14.720050Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Bioreason-pro: Advancing protein function prediction with multimodal biological reasoning.bioRxiv","venue":null,"work_id":"8fb8a507-a4c9-4b65-b0ef-447f678f33a0","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":24,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:9cd00b54cfc78e5b741377ccec8db304b1b7266392001dfd8d2c84c2b58e9443","observation_id":"dee76677-8a3b-46c4-97a3-7de9508f7655","resolution":{"observed_at":"2026-05-14T22:48:14.577095Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2306.08018","last_updated":"2024-03-04T12:49:31Z","snapshot_observed_at":"2026-08-13T11:18:08.460930Z","submitted_at":"2023-06-13T14:35:34Z","title":"Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models","version":5},"cited_work":{"arxiv_id":"2306.08018","doi":"10.48550/arxiv.2306.08018","metadata_source":"arxiv_reference","pith_arxiv_id":"2306.08018","snapshot_observed_at":"2026-08-05T02:28:24.338817Z","title":"arXiv preprint arXiv:2306.08018 , year=","venue":"arXiv (Cornell University)","work_id":"4358caf5-5816-492a-8e16-0653a61fdac8","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":25,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2306.08018","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:305f68e2967d4b8bc920db62bbc1c002af13846ab99432c2b94b9d285f545252","observation_id":"9e010514-8e80-4c51-9b73-820c33f4d6e3","resolution":{"observed_at":"2026-05-14T22:13:04.885267Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protgpt2 is a deep unsupervised language model for protein design.Nature communications, 13(1):4348","venue":null,"work_id":"52989572-5dbc-4208-817f-d97ac7837aef","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":26,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:136431b4e7c07a1ac6c08db83f2379e7360f0d18c7856c24712784c2dcc9cecc","observation_id":"fd8eada7-49ec-4d24-8dd3-9548ace02636","resolution":{"observed_at":"2026-05-14T22:48:14.581141Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":null,"venue":null,"work_id":"8769c93a-edf1-4cc7-8993-b4b6d7baee75","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":27,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6c949d16d8d99d04410e40cad2e04ce710e3a2db7e7a86092b685b1985f7533c","observation_id":"febd8d9b-9260-4c30-bfe6-b954daab1075","resolution":{"observed_at":"2026-05-14T22:48:14.668568Z","resolver_source":"raw_fallback","status":"unresolved"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-08T12:44:53.492909Z","title":"Structure-based protein function prediction using graph convolutional networks.Nature communications, 12(1):3168","venue":null,"work_id":"31249243-f280-4f8a-a149-1a54e904ad6b","year":2021},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":28,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:2ae0a1fdf67fd5dd9e7e226e350094258c3f4cc8d142cd4df1e563c85ba18de0","observation_id":"d935af2b-d291-4158-bf6d-0f78e275b597","resolution":{"observed_at":"2026-05-14T22:48:14.761708Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protein engineering for industrial biocatalysis: principles, approaches, and lessons from engineered petases.Catalysts, 15(2):147","venue":null,"work_id":"34927cca-b204-47ef-92a5-2efeaaf19470","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":29,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:56023b1bd8c72c80643676c1d16f60457ffb074501716880b2e2cc6fd6db5c77","observation_id":"cf96cb01-3eec-45ef-8e3b-b06483baa877","resolution":{"observed_at":"2026-05-14T22:48:14.609618Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protein design with guided discrete diffusion","venue":null,"work_id":"dfa8d30e-d593-4113-88c2-dbafccd4c353","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":30,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:862b3bbe6ddee70a2f92734da4d08ff54779ec8e5ffe85d2ea379cbb08efdf4d","observation_id":"0c5e495d-c7ce-4eaa-8f14-072efcbd4647","resolution":{"observed_at":"2026-05-14T22:48:14.568463Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"pykvfinder: an efficient and integrable python package for biomolecular cavity detection and characterization in data science.BMC bioinformatics, 22(1):607","venue":null,"work_id":"9d242156-7356-4b08-960b-3781064a75bf","year":2021},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":31,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f3b5fb41b65a76af1de0eefc4b4c99004b672bff9ac69f470279d87bfc21f5d8","observation_id":"01d1d0cb-d835-4d9b-b125-c8fadc4303e1","resolution":{"observed_at":"2026-05-14T22:48:14.594443Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Learning sequence, structure, and function representations of proteins with language models.bioRxiv","venue":null,"work_id":"cb0330cf-6a57-4e4c-a5c6-b6dfe56a82b0","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":32,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:62b38088c89cf2b223aa5ad8efb464efd55c8c04e8d8cbd21598191c269cc9d7","observation_id":"3c9f6b84-146e-459a-b583-cde152189401","resolution":{"observed_at":"2026-05-14T22:48:14.664433Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-08T12:44:54.321505Z","title":"Simulating 500 million years of evolution with a language model.Science, 387(6736):850–858","venue":null,"work_id":"30050362-f781-47b2-a9aa-88655da87165","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":33,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:a1edd0cda0dbe6dc897ee0776d5c3c880b8a8c239e2b5828292c98d110c52a80","observation_id":"28fa967b-7102-4108-8689-eaca441c95cd","resolution":{"observed_at":"2026-05-14T22:48:14.790683Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Efficient evolution of human antibodies from 11 general protein language models.Nature biotechnology, 42(2):275–283","venue":null,"work_id":"7633fccc-a74f-42a9-9090-90ac5d0cbe9a","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":34,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f56389945220a6ee60bfbf5046a069394a23e8f44b1b68695111b7aac3124041","observation_id":"0a70a71c-f798-44af-b5f0-5a2fbfde7a24","resolution":{"observed_at":"2026-05-14T22:48:14.786828Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Adaptive machine learning for protein engineering.Current opinion in structural biology, 72:145–152","venue":null,"work_id":"15fcf833-72a8-4a96-a1b9-c10d12bdfcf7","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":35,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:a2a5db87d1ead32d29c4ffe0f0c88353dcf0f62f716e8062fa1287dab7285893","observation_id":"01cd49a8-82be-4474-8df5-b0143ed2c0e0","resolution":{"observed_at":"2026-05-14T22:48:14.770109Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Pro-1.https://michaelhla.com/blog/pro1.html, March 2025","venue":null,"work_id":"e9240c77-d1e9-4844-8c7e-4cb941a34374","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":36,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:3f3c0ddf2942d081ca216784e94c832ca567b71d89b9bbe2d7df675c8c903968","observation_id":"eeca7ea1-1766-4d55-9907-9ef38702638f","resolution":{"observed_at":"2026-05-14T22:48:14.735266Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2504.11454","last_updated":"2025-06-12T00:51:35Z","snapshot_observed_at":"2026-08-12T14:50:28.552854Z","submitted_at":"2025-04-15T17:59:43Z","title":"Elucidating the Design Space of Multimodal Protein Language Models","version":3},"cited_work":{"arxiv_id":"2504.11454","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2504.11454","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Elucidating the design space of multimodal protein language models","venue":null,"work_id":"855414b8-36ca-4dd2-89ee-9459b1967361","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":37,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2504.11454","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:74f00501af6941e036cc42793894af371a3c8b72aa3384ec8fdf582c671f2c07","observation_id":"f867223a-a1d3-4106-8a1b-3b32ae7e589f","resolution":{"observed_at":"2026-05-14T22:13:04.858356Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protein2text: Resampling mechanism to translate protein sequences into human-interpretable text","venue":null,"work_id":"9b2e3250-1e19-4a3e-83eb-98ac17a22511","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":38,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:2e0601aacea3266adda969f95afe4b790c30c4395c6beb8dff4e56a9233431bf","observation_id":"7584d80e-0464-4736-867b-e4d0b70e0db3","resolution":{"observed_at":"2026-05-14T22:48:14.542841Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"A multi-modal llm for dynamic protein-ligand interactions and generative molecular design.bioRxiv","venue":null,"work_id":"cd0f69c5-cc84-46c2-9605-ae055fdf0631","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":39,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:77cc6a1530353945a5edfd9b92436d8f8bbd8fb418fbf105e4ac6841ce5226a3","observation_id":"16aa8b8b-d518-4467-af36-5a9edf39421b","resolution":{"observed_at":"2026-05-14T22:48:14.613706Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Dictionary of protein secondary structure: pattern recogni- tion of hydrogen-bonded and geometrical features.Biopolymers, 22(12):2577–2637","venue":null,"work_id":"ccdd1ff0-2d14-4636-ae55-0a493a336732","year":1983},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":40,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b7612137e97f6689ae144229c50e2a5769de86fc2fcf26d4d455950915850812","observation_id":"ffd24cd8-d370-4a61-9a15-79005bc5e6ea","resolution":{"observed_at":"2026-05-14T22:48:14.707032Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Pubchem 2023 update","venue":null,"work_id":"5f076793-1d58-496c-8732-3e99ebac27f5","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":41,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f15f12834dbe9681d05cac8b0a3aba7a3ba07c9b2f5572f0d9d52ab7fb360b03","observation_id":"fd24e244-dfdf-441a-81ce-d0413e693e0c","resolution":{"observed_at":"2026-05-14T22:48:14.680926Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2307.00494","last_updated":"2024-03-03T00:32:07Z","snapshot_observed_at":"2026-08-13T11:04:24.036702Z","submitted_at":"2023-07-02T06:55:31Z","title":"Improving Protein Optimization with Smoothed Fitness Landscapes","version":3},"cited_work":{"arxiv_id":"2307.00494","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2307.00494","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Improving protein optimization with smoothed fitness landscapes","venue":null,"work_id":"0d05befd-d83c-45e0-b5b8-7611c842aaff","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":42,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2307.00494","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:97dba548055ffe27a9b9f81de0c1617e3a1c5f9006272d8e00f1b46efa3c936a","observation_id":"81e5a623-df66-4394-a761-8f21641df4e2","resolution":{"observed_at":"2026-05-14T22:13:04.871768Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Sequence-structure-function relationships in the microbial protein universe.Nature communications, 14(1):2351","venue":null,"work_id":"af20c145-f7de-46eb-9ca6-0855e981819d","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":43,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f2435557e715561baad0588fa3d155b257f157e4db834d061ad6dbda22f55517","observation_id":"0b0060cb-7ef4-4ee4-8624-f1c48ff5236f","resolution":{"observed_at":"2026-05-14T22:48:14.688347Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Rational and semirational protein design.Protein engineering: methods and protocols, pages 15–23","venue":null,"work_id":"287f73dc-548a-47ea-8be1-c831b6fb72e6","year":2017},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":44,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:23575abb229cd29a5841908cff4c4b0f950d8c56299fa1db5302f14933bd5dfa","observation_id":"42fe43af-1bed-4ed9-9afa-1d1b55627dc0","resolution":{"observed_at":"2026-05-14T22:48:14.598832Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"De novo protein design—from new structures to programmable functions","venue":null,"work_id":"8a4ef69a-1a6b-4ca0-b086-da4ee69d887c","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":45,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:406f4ad330f47fd4363f13f517c8391d55e130786ed2f6119ff88b2814631d9f","observation_id":"736b704d-986e-4a4a-8169-19912862cd05","resolution":{"observed_at":"2026-05-14T22:48:14.618030Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2505.20346","last_updated":"2026-07-04T06:08:39Z","snapshot_observed_at":"2026-08-07T14:20:14.247577Z","submitted_at":"2025-05-25T05:40:15Z","title":"PDFBench: A Benchmark for De novo Protein Design from Function","version":3},"cited_work":{"arxiv_id":"2505.20346","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2505.20346","snapshot_observed_at":"2026-07-07T03:17:09.828184Z","title":"Pdfbench: A benchmark for de novo protein design from function","venue":null,"work_id":"196ed635-98c2-462a-8981-1f6d53474edc","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":46,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2505.20346","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:7375ac21d1810e6d9e199db66342e5e97443794cee0081be49373a836c0d165f","observation_id":"db546d35-0593-4342-9849-ecf83a1d8467","resolution":{"observed_at":"2026-07-07T03:17:09.828184Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Conditional generative modeling for de novo protein design with hierarchical functions.Bioinformatics, 38(13):3454– 3461","venue":null,"work_id":"9f31e6a6-14ca-491f-9571-5d3eca067582","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":47,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:24b7c5434e003b79b7850236b1169fd88626eeb49b2cf96d5b81c112c1611c22","observation_id":"36c87f6b-3eed-425a-8b21-58d0f18b5b14","resolution":{"observed_at":"2026-05-14T22:48:14.552408Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Design of a novel globular protein fold with atomic-level accuracy.Science, 302(5649):1364–1368","venue":null,"work_id":"6879ba3c-edf3-47cf-94f8-b99159096f06","year":2003},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":48,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:22844c1b71abf2670863aa4d81e5dd805be9f6833c8cc0513a4e455d4e0200f2","observation_id":"cee39a3c-b66c-4bba-a945-182561a48860","resolution":{"observed_at":"2026-05-14T22:48:14.623928Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2502.19173","last_updated":"2025-02-26T14:31:21Z","snapshot_observed_at":"2026-08-14T05:42:52.085094Z","submitted_at":"2025-02-26T14:31:21Z","title":"A Model-Centric Review of Deep Learning for Protein Design","version":1},"cited_work":{"arxiv_id":"2502.19173","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2502.19173","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"A model-centric review of deep learning for protein design","venue":null,"work_id":"3e83d156-49a4-4364-82f1-d66e093b4d39","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":49,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2502.19173","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:86eb2226bbc4fb86285d0de9d6e65ea8e9ab32db5be39088a4a4f553f1322c17","observation_id":"33b96e3e-d1dd-4b24-abb9-88f0e313aa1d","resolution":{"observed_at":"2026-05-14T22:13:04.831390Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules","venue":null,"work_id":"5c6840e2-4277-48a6-aa35-cf4aa3b7cab6","year":2011},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":50,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:e3adccdf4a47b09ea9dda7684a42d1bf271b8d273cf46ec9c6592ec9f4d5baa4","observation_id":"9d21f5b4-927e-44ef-b004-edf58ebf886e","resolution":{"observed_at":"2026-05-14T22:48:14.782823Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2512.02556","last_updated":"2025-12-02T09:25:14Z","snapshot_observed_at":"2026-08-12T08:24:59.243273Z","submitted_at":"2025-12-02T09:25:14Z","title":"DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models","version":1},"cited_work":{"arxiv_id":"2512.02556","doi":"10.18653/v1/d18-1512","metadata_source":"pith","pith_arxiv_id":"2512.02556","snapshot_observed_at":"2026-08-05T02:28:24.338817Z","title":"DeepSeek-V3.2: Pushing the Frontier of Open Large Language Models","venue":"cs.CL","work_id":"07c85cc5-4086-4abc-823b-6d0f4ff784d0","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":51,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2512.02556","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:fb1b7641c967d4c20c0f44e0527cb1b380e90ee4886ceb81bd2e5f958f602d8f","observation_id":"2fca31fb-db2b-4cf2-ab5b-bc2517e4f7e1","resolution":{"observed_at":"2026-05-14T22:13:04.851681Z","resolver_source":"local_arxiv","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protein design with dynamic protein vocabulary","venue":null,"work_id":"4e5af913-de34-4249-8f82-092e643ff181","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":52,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:046ff053b960379d13e2d58e4165add8d5fe85c4072092b054395e38c91053b9","observation_id":"4bca2dcb-27fd-4454-9f75-1449f56e40a9","resolution":{"observed_at":"2026-05-14T22:48:14.519893Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"A text-guided protein design framework","venue":null,"work_id":"cc95a2b4-d040-4fee-8533-50947cff56ee","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":53,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:fab53a647b1134ff802b824632a8164cecc51842abbf81edff946e0a71436543","observation_id":"514dc0d0-2e6d-4b5b-8aaa-efab4b9d6b72","resolution":{"observed_at":"2026-05-14T22:48:14.485480Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Prollama: A protein large language model for multi-task protein language processing.IEEE Transactions on Artificial Intelligence","venue":null,"work_id":"156cd22d-ed61-4722-934e-a2a6d2df6e83","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":54,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:bd171b6415d519e98e2dc27ccbd7da80e9e9f50444ff6ec7e48b6d60dcb68633","observation_id":"293fee1a-578e-4632-b8e3-d33184d6d59e","resolution":{"observed_at":"2026-05-14T22:48:14.563639Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Prottex: Structure-in-context reasoning and 12 editing of proteins with large language models.Journal of Chemical Information and Modeling, 65(13):6599–6612","venue":null,"work_id":"09f66981-0749-48b1-af22-5d829062d148","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":55,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:ec889f6c66801f2488541fdec9936d5fe607db915dbbe23143a32a65d2f7f3fd","observation_id":"7b0ab329-9550-40fc-a5f0-d104121249d5","resolution":{"observed_at":"2026-05-14T22:48:14.572677Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Zymctrl: a conditional language model for the controllable generation of artificial enzymes","venue":null,"work_id":"bb6d866b-1f75-4be6-b237-ee8641697c91","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":56,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:75615e0c32fe1c3ffec05da72138cb2b0cb585f6fcb09211cbb4288a565bb632","observation_id":"bdcb992b-4fe1-41d6-9226-7fc8703e690e","resolution":{"observed_at":"2026-05-14T22:48:14.715225Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-06T14:32:35.669223Z","title":"Progen2: exploring the boundaries of protein language models.Cell systems, 14(11):968–978","venue":null,"work_id":"3e4f96b5-cf4c-44eb-b9c6-a9687d70f1f8","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":57,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:e701e4b1d9a93bb46eb92a6dfee5896666d46cb79bdcbe8195e9ef34c2074ca4","observation_id":"250d7380-a50f-4c42-89ae-897e4cf90924","resolution":{"observed_at":"2026-05-14T22:48:14.728593Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Machine learning for functional protein design.Nature biotechnology, 42(2):216–228","venue":null,"work_id":"3de5f657-ae37-43ff-b7db-e514f16820e1","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":58,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:55353b1df30756d315bbaafe4b41623fe753f9b7278a2cf85c9ea99cf86b7295","observation_id":"2d1c5d87-6719-4e98-8fb3-f014147a07ec","resolution":{"observed_at":"2026-05-14T22:48:14.753676Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Accelerating life sciences research with retro biosciences","venue":null,"work_id":"5825ce43-cc81-46cf-8330-bb3eadd05935","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":59,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:4b8b7d5416050d8da298c2dbda019dbf86a96ef3f96372bf2196edacdff8f618","observation_id":"1cb032ab-dee1-46a3-965f-482123a9a68f","resolution":{"observed_at":"2026-05-14T22:48:14.672820Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Introducing gpt-5","venue":null,"work_id":"dcc86da7-87fb-4c2c-8834-d2027a1f2433","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":60,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:9eea28dbb7cb7d4467157ec11b8d19fa7155fdfa69f0f8d642858360547b76f7","observation_id":"425a45ec-00af-4aff-a764-92ea3448ba23","resolution":{"observed_at":"2026-05-14T22:48:14.676974Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Introducing gpt-rosalind for life sciences research","venue":null,"work_id":"56633400-4ebe-4ddd-9b8b-e75518419973","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":61,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b75612de8cf6c265c3fc0a7fcd9f1f6124a6cb658ad04ba35cc58dce90b2f61b","observation_id":"f12400c0-51dd-421c-b63a-c0e5abc3e18d","resolution":{"observed_at":"2026-05-14T22:48:14.628064Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Design and engineering of miniproteins.ACS bio & med Chem Au, 2(4):316–327","venue":null,"work_id":"569bd057-025a-4c37-988e-991091d8dedf","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":62,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:545131002a79782e7dd1a6f494e479b05ae828839c9e3e54f3469816178a5188","observation_id":"7c582a07-76ed-4a82-9e10-fd4c49fa6425","resolution":{"observed_at":"2026-05-14T22:48:14.506647Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Bindcraft: one-shot design of functional protein binders.BioRxiv, pages 2024–09","venue":null,"work_id":"9de1877b-95cf-4002-8c5e-cd3039dfaac7","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":63,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:ccc914047e13db824d986232e68694bf9778e1adc82bb4c9fea539c82eedc406","observation_id":"4b1236ea-0dfd-49bb-ae0f-6401dbb009e5","resolution":{"observed_at":"2026-05-14T22:48:14.556945Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Proteincrow: A language model agent that can design proteins","venue":null,"work_id":"0e49b49c-327b-465c-9c0f-7393d6b0b812","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":64,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:95b28afff310de73ff7f67e23b00772caf79130e4939075e6f410538603e1f9b","observation_id":"489f8559-0830-4982-b606-bbe160f4d69a","resolution":{"observed_at":"2026-05-14T22:48:14.604745Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Qwen3.5: Towards native multimodal agents","venue":null,"work_id":"fc31141f-ef12-4061-b47d-6e52418f3cba","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":65,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:2fdf9a951f041354cff93f2b91a305fc9b5ec3a4d88cac10d29ae46466a258e1","observation_id":"8bbe2072-e064-4b20-856b-4f92fca102b6","resolution":{"observed_at":"2026-05-14T22:48:14.502604Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"A generalized protein design ml model enables generation of functional de novo proteins","venue":null,"work_id":"cc7f97bf-07b6-412e-aa8e-c91faf4c055d","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":66,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:a6f72c97edb081684577f7be668a0865ea8c974da79096ff3bc22e0d09082c51","observation_id":"2475b75a-d128-4a1a-bc89-37d9d527a89c","resolution":{"observed_at":"2026-05-14T22:48:14.510868Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":"2512.22257","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-04T07:49:39.632854Z","title":"Liveproteinbench: A contamination-free benchmark for assessing models’ specialized capabilities in protein science","venue":null,"work_id":"73c690c8-ebb7-49e5-9c1e-aafe3c2bf479","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":67,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:1367dd776404821ed4af56da2f864cda625396df25a2cf77d0df46b660eb8580","observation_id":"3285ef1c-f925-492c-bab9-c794aa525abd","resolution":{"observed_at":"2026-05-14T22:13:04.838241Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protein sequence design and its applications.Current opinion in structural biology, 37:71–80","venue":null,"work_id":"f5a60c91-4aa5-476b-b618-779b3e0beeff","year":2016},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":68,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:954c07eab88ae82ca876c6525a88d81d7775e1de05230def8e989ce96cdc501a","observation_id":"b40e6653-be43-49d0-8c7f-008c000990fd","resolution":{"observed_at":"2026-05-14T22:48:14.524966Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Improved protein binder design usingβ-pairing targeted rfdiffusion.Nature Communications","venue":null,"work_id":"69a3b812-7d5f-4fe9-863b-c4288456c377","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":69,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f31e53955f276905ecb6f974ba8cf6d3952f9440a4756013f5afd20594add0a5","observation_id":"a03e6803-e16c-4b10-b175-32ea43f3d8c0","resolution":{"observed_at":"2026-05-14T22:48:14.475917Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-07T21:54:08.939333Z","title":"Brenda, the enzyme database: updates and major new developments","venue":null,"work_id":"a81b7a68-6231-4e81-9ef7-b61037f72923","year":2004},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":70,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:65e0191a9520ed706907eb7c19b230e934d4435324b8aca41f8ff594e982e5c2","observation_id":"723f1884-8248-4afd-bf20-c39196da2bd2","resolution":{"observed_at":"2026-05-14T22:48:14.533638Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"A fine-tuning dataset and benchmark for large language models for protein understanding","venue":null,"work_id":"564809fd-5e00-4beb-8c39-d7c28023b376","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":71,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:7d855e774dddc8c7976276e13fd88b158e0eb117f244948ccc3ed2219861cc9b","observation_id":"e9f7580f-f53d-42c7-887f-3eccb5a8ff84","resolution":{"observed_at":"2026-05-14T22:48:14.515523Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Toursynbio: A multi-modal large model and agent framework to bridge text and protein sequences for protein engineering","venue":null,"work_id":"03e79d9f-eb03-4d33-b987-9bb63cdfe04f","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":72,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6c29e6ea81a1aebee5bf480c2755ad24c6edcfbedc2a2f15993b017689622563","observation_id":"07e7b074-bd92-43da-89ec-d8aa4f92c858","resolution":{"observed_at":"2026-05-14T22:48:14.589622Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"New and continuing developments at prosite.Nucleic Acids Research, 41(D1):D344–D347","venue":null,"work_id":"e3f4c301-fd89-43ef-9c6c-822e6b71841b","year":2013},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":73,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:57aa20e53f9d73d3b61e8138da3a733fc8cee18abb455122b127bd32a3319636","observation_id":"16052600-744f-4d3e-8355-c58f06a08bc1","resolution":{"observed_at":"2026-05-14T22:48:14.697845Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2512.15930","last_updated":"2026-04-27T15:49:06Z","snapshot_observed_at":"2026-08-11T11:25:08.086477Z","submitted_at":"2025-12-17T19:55:04Z","title":"Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins","version":2},"cited_work":{"arxiv_id":"2512.15930","doi":null,"metadata_source":"pith","pith_arxiv_id":"2512.15930","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Scalable Agentic Reasoning for Designing Biologics Targeting Intrinsically Disordered Proteins","venue":"q-bio.QM","work_id":"dfa06799-dde3-489a-81ee-7b1ac52139df","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":74,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2512.15930","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:75f6254e8b48e7804c913e9a5c1d87105313eb1ae5c57e77466a66eef5cccb9f","observation_id":"08cbc073-067c-4565-b6a3-3845467b9807","resolution":{"observed_at":"2026-05-14T22:13:04.804937Z","resolver_source":"local_arxiv","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":"2506.09332","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Instructpro: Natural language guided ligand-binding protein design","venue":null,"work_id":"542c2165-2ea1-4b18-b98e-85d71ac35be8","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":75,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6ec5ac5fbfae1c86fb5d366775823dcec0eaf3807269198557982680015c477e","observation_id":"2326aa63-ca4c-490c-b864-7df17afcf81f","resolution":{"observed_at":"2026-05-14T22:13:04.797578Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Boltzgen: Toward universal binder design.bioRxiv, pages 2025–11","venue":null,"work_id":"ea04f847-6c4c-481d-943b-2eaad465ea8d","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":76,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:e5c90337f8843943eb6ff6d10ec8c5d18194f59e4f0a3d519fc6195ab9af793d","observation_id":"b5ba26ae-6ee6-431d-a434-0cf97ef81e3b","resolution":{"observed_at":"2026-05-14T22:48:14.743213Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2503.15438","last_updated":"2025-03-19T17:19:07Z","snapshot_observed_at":"2026-08-13T04:59:08.415697Z","submitted_at":"2025-03-19T17:19:07Z","title":"VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning","version":1},"cited_work":{"arxiv_id":"2503.15438","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2503.15438","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Venusfactory: A unified platform for protein engineering data retrieval and language model fine-tuning","venue":null,"work_id":"472f5556-36d9-40ad-bc94-01b6cd849a39","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":77,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2503.15438","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:571f4a23a791557497599af760c9055bdf1bf2c7d4cd72c847a2e77c53c0791a","observation_id":"03aa770c-a278-444a-ad1d-05f53f29cbc9","resolution":{"observed_at":"2026-05-14T22:13:04.791414Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2602.02276","last_updated":"2026-02-02T16:17:38Z","snapshot_observed_at":"2026-08-12T00:25:39.214406Z","submitted_at":"2026-02-02T16:17:38Z","title":"Kimi K2.5: Visual Agentic Intelligence","version":1},"cited_work":{"arxiv_id":"2602.02276","doi":"10.48550/arxiv.2602.02276","metadata_source":"pith","pith_arxiv_id":"2602.02276","snapshot_observed_at":"2026-08-05T02:28:24.338817Z","title":"Kimi K2.5: Visual Agentic Intelligence","venue":"cs.CL","work_id":"d690be8f-5d53-49b0-b1e7-79668eb8fcdb","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":78,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2602.02276","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:71ec41294652df72c54f080cebfe08003eb05bb36a3ffc23937a9e45e7d78f62","observation_id":"5acef15e-4a4a-46bb-8148-9239439c847d","resolution":{"observed_at":"2026-05-14T22:13:04.766863Z","resolver_source":"local_arxiv","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-07T20:38:24.673777+00:00","source":"crossref_status_cache"},{"observed_at":"2026-08-07T20:38:24.673777+00:00","source":"openalex_status_cache"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protenix-v1: Toward high-accuracy open-source biomolecular structure prediction.bioRxiv","venue":null,"work_id":"88e7a299-2033-4eb7-a412-8d15c59499e0","year":2026},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":79,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f2d4499db4133f186e364ae65fe664045ae309c07e9412c05efeb25056072e2e","observation_id":"33cc894f-6a16-4631-a4b3-856bd2301cec","resolution":{"observed_at":"2026-05-14T22:48:14.778368Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Engineering strategies to overcome the stability–function trade-off in proteins.ACS synthetic biology, 11(3):1030–1039","venue":null,"work_id":"16d00d8f-88f6-49c1-8b02-a39db62c3c3b","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":80,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:5a16d4004251c9a4e0cbead248e74630f5c4a4960144dd7a84e48c11fc6dcf4c","observation_id":"221bb19e-a811-49ba-956a-3175834b2805","resolution":{"observed_at":"2026-05-14T22:48:14.651389Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Uniprot: the universal protein knowledgebase in 2023.Nucleic Acids Research, 51(D1):D523–D531","venue":null,"work_id":"b86e48d1-c8d8-447d-b11c-1f5fa16d2f05","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":81,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6c41f737b03e6f4e8d2addc772ee913e88f72f3d962949ce0498d01abc01465a","observation_id":"d5141968-7dcc-4164-ad04-a5f02f8a5f39","resolution":{"observed_at":"2026-05-14T22:48:14.765873Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":null,"venue":null,"work_id":"e5bf1bef-8473-4d80-ab7f-1c4b519e3647","year":2010},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":82,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b70309360987837db6a72c7aecf52b8d3cd8fb78f0a5fa320d1d8e0165f6252d","observation_id":"8e04fc1e-0179-44d1-b3eb-abd1e030fc81","resolution":{"observed_at":"2026-05-14T22:48:14.584974Z","resolver_source":"raw_fallback","status":"unresolved"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2312.00080","last_updated":"2023-11-30T02:37:55Z","snapshot_observed_at":"2026-08-13T05:13:53.039713Z","submitted_at":"2023-11-30T02:37:55Z","title":"PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design","version":1},"cited_work":{"arxiv_id":"2312.00080","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2312.00080","snapshot_observed_at":"2026-06-29T19:33:54.341621Z","title":"Pdb-struct: A comprehensive benchmark for structure-based protein design","venue":null,"work_id":"c63c4888-6f34-406c-aa70-818eff41265c","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":83,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2312.00080","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b9e447b511099bd82f9e766736ff624a3d03a329badde72cb6171cf739b4cca1","observation_id":"039b2f0e-3250-429e-b7ff-e0a1552031f6","resolution":{"observed_at":"2026-05-14T22:13:04.778579Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2504.06196","last_updated":"2025-04-08T16:39:02Z","snapshot_observed_at":"2026-08-11T23:16:32.962813Z","submitted_at":"2025-04-08T16:39:02Z","title":"TxGemma: Efficient and Agentic LLMs for Therapeutics","version":1},"cited_work":{"arxiv_id":"2504.06196","doi":"10.48550/arxiv.2504.06196","metadata_source":"arxiv_reference","pith_arxiv_id":"2504.06196","snapshot_observed_at":"2026-08-05T02:28:24.338817Z","title":"Txgemma: Efficient and agentic llms for therapeutics","venue":"ArXiv.org","work_id":"bde80c51-ba33-41ed-bb94-990fd2acfdfe","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":84,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2504.06196","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:b690b00419848f871b5b004f00a0b9fd1d5213b9a48bd642742409f097203221","observation_id":"c7a36dfc-c8f2-46d7-bf86-d7b36c45273d","resolution":{"observed_at":"2026-05-14T22:13:04.824726Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":"2511.22311","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-04T13:29:51.462176Z","title":"Y ., Lee, D","venue":null,"work_id":"55d259c2-5523-49b7-a319-bbfb7385aafa","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":85,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:863b81059344e5c90ee61b7d210ba3d3e199d12c99acd4ced257aeb690212e0a","observation_id":"b2f18d74-c1d6-4cf2-bb7e-c1aefa3f0bf3","resolution":{"observed_at":"2026-05-14T22:13:04.818429Z","resolver_source":"arxiv_id","status":"metadata_mismatch"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":"2509.21320","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-07-04T08:19:44.760572Z","title":"Scireasoner: Laying the scientific reasoning ground across disciplines","venue":null,"work_id":"d4a82cd2-3f60-44a9-a49d-16b6dffedcf5","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":86,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:1c92d9780bf2c211582c88c3f942f2943e39a32f0a7ca6911d5d829102633b86","observation_id":"99f57a8c-7496-4b8e-8806-62fa98dd0e5e","resolution":{"observed_at":"2026-05-14T22:13:04.811774Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Rethinking text-based protein understanding: Retrieval or llm? InProceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, pages 23737–23757","venue":null,"work_id":"9a600c23-f693-4bf1-886a-9502549b84fd","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":87,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:7fcf80f766b2e3594ebb2eae1349e20fa5f4b35159d93512157e139dc7874b58","observation_id":"419c3b20-a877-446b-bf5f-224e9a703bb6","resolution":{"observed_at":"2026-05-14T22:48:14.656043Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2502.07527","last_updated":"2025-06-20T05:18:13Z","snapshot_observed_at":"2026-08-09T17:43:38.820458Z","submitted_at":"2025-02-11T13:08:03Z","title":"Nature Language Model: Deciphering the Language of Nature for Scientific Discovery","version":3},"cited_work":{"arxiv_id":"2502.07527","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2502.07527","snapshot_observed_at":"2026-07-04T08:19:44.796752Z","title":"Zhangchen Xu, Yang Liu, Yueqin Yin, Mingyuan Zhou, and Radha Poovendran","venue":null,"work_id":"a990f4f1-c3a1-41ea-aca0-c563c5520b57","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":88,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2502.07527","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:cd1dbcec73a2f193b91b42e84648e58c4c9c9e9e7868c5038505cf7b28585b69","observation_id":"6b329ca3-78cb-49a7-9aee-b95ae086d122","resolution":{"observed_at":"2026-05-14T22:13:04.772627Z","resolver_source":"arxiv_id","status":"metadata_mismatch"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2408.11363","last_updated":"2025-04-17T21:55:37Z","snapshot_observed_at":"2026-08-12T23:00:13.035658Z","submitted_at":"2024-08-21T06:16:22Z","title":"ProteinGPT: Multimodal LLM for Protein Property Prediction and Structure Understanding","version":2},"cited_work":{"arxiv_id":"2408.11363","doi":"10.48550/arxiv.2408.11363","metadata_source":"arxiv_reference","pith_arxiv_id":"2408.11363","snapshot_observed_at":"2026-08-05T02:28:24.338817Z","title":"ProteinGPT: Multimodal LLM for protein property prediction and structure understanding","venue":"arXiv (Cornell University)","work_id":"f4b9c99e-28b4-48ff-8f60-93ee3d15659b","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":89,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2408.11363","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:cc7dc504bd0cc6a4bbb13ad13f65749be2254de0810e13d187336f63762a763a","observation_id":"18e72b7a-a282-432b-8428-0db7ba98d039","resolution":{"observed_at":"2026-05-14T22:13:04.784926Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protst: Multi-modality learning of protein sequences and biomedical texts","venue":null,"work_id":"bcf500be-0e60-488f-b221-15a0f8f62f76","year":2023},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":90,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:0419ccac13e3fbda036f879418e99849dfe1c313d164824de6492b428aceafb8","observation_id":"16c0d3be-21a9-412f-acc5-53b36e0df916","resolution":{"observed_at":"2026-05-14T22:48:14.537591Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Peer: a comprehensive and multi-task benchmark for protein sequence understanding","venue":null,"work_id":"965d2df1-21b4-4258-ba94-c8b10888a4ff","year":2022},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":91,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:611fbe20f33e355325ab49c2eaa851b3dd6bae85d0f16ea231ea0da803f32faf","observation_id":"8bb1f607-ba97-497a-abbe-dcb1dcaf097a","resolution":{"observed_at":"2026-05-14T22:48:14.490038Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2410.03634","last_updated":"2025-06-11T23:50:48Z","snapshot_observed_at":"2026-08-13T04:59:32.785978Z","submitted_at":"2024-10-04T17:41:47Z","title":"Function-Guided Conditional Generation Using Protein Language Models with Adapters","version":2},"cited_work":{"arxiv_id":"2410.03634","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2410.03634","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Function-guided conditional generation using protein language models with adapters","venue":null,"work_id":"1b56574b-495c-4dbd-ad1a-37cff5a0b353","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":92,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2410.03634","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:851872a11a545088e0faa9e853edf75947026ae5c131de2d0a0fbb1285abd1dc","observation_id":"33a1834c-243a-479d-afa7-e6ddeaa7490b","resolution":{"observed_at":"2026-05-14T22:13:04.891990Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Care: a benchmark suite for the classification and retrieval of enzymes","venue":null,"work_id":"c759a9f5-0542-4129-a525-e551724dcc98","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":93,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:9684fdf04ed931a24821152ccab57e94a1728baca79dc53ac1bbf722f8616435","observation_id":"881a6790-a6c6-4f4e-b918-e74f5c4125f7","resolution":{"observed_at":"2026-05-14T22:48:14.494484Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2409.06744","last_updated":"2024-10-07T08:20:32Z","snapshot_observed_at":"2026-08-12T22:48:00.905679Z","submitted_at":"2024-09-10T06:52:33Z","title":"ProteinBench: A Holistic Evaluation of Protein Foundation Models","version":2},"cited_work":{"arxiv_id":"2409.06744","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2409.06744","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Proteinbench: A holistic evaluation of protein foundation models","venue":null,"work_id":"68d30fa4-e08d-4d9d-8882-bf51c587df2b","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":94,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2409.06744","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:40a2e61f5f5ff07e09e0a08ceb8c7c4800ca27453b55b1f42e8567521cb8fd93","observation_id":"e0a6d09f-028a-4892-87ac-3557afe07028","resolution":{"observed_at":"2026-05-14T22:13:04.865213Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Annotation-guided protein design with multi-level domain alignment","venue":null,"work_id":"121512f4-40cc-417e-bd47-9ae5a4586529","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":95,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:1ebda6faccc88fff9a6927b113fa8d008542de9e27358f29ec603232495fac23","observation_id":"275e7f10-edde-493b-8778-c0da8fa516b8","resolution":{"observed_at":"2026-05-14T22:48:14.498578Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":{"arxiv_id":"2503.06687","last_updated":"2025-08-26T13:21:39Z","snapshot_observed_at":"2026-08-13T04:59:08.333147Z","submitted_at":"2025-03-09T16:43:07Z","title":"UniGenX: a unified generative foundation model that couples sequence, structure and function to accelerate scientific design across proteins, molecules and materials","version":2},"cited_work":{"arxiv_id":"2503.06687","doi":null,"metadata_source":"arxiv_reference","pith_arxiv_id":"2503.06687","snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":null,"venue":null,"work_id":"0127f494-0d56-4452-b43b-f9c41ce4badf","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":96,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"cited_paper":"/paper/2503.06687","citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f056ded16a7b9819edbab1ce9a9f747d22933068e80fa6d36bffabb0d5191fa2","observation_id":"bb25ce63-5d3a-4bb4-855b-adeb443f0a50","resolution":{"observed_at":"2026-05-14T22:13:04.878158Z","resolver_source":"arxiv_id","status":"verified_exact"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Sglang: Efficient execution of structured language model programs","venue":null,"work_id":"6a37eae9-6f5e-4ce8-ac0a-999538290076","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":97,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:1f2e2c2d9e6301c0d7c4aef795bc7f7020a09d647293b1da666f327ceb8ae58d","observation_id":"113b5369-8fbb-4b5c-b621-9ecf30212ee5","resolution":{"observed_at":"2026-05-14T22:48:14.529474Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Decoding the molecular language of proteins with evolla.bioRxiv, pages 2025–01","venue":null,"work_id":"2ade4fed-d762-429a-bf44-1bf84191e9b3","year":2025},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":98,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:f38e0641afab8e82eb2bf806563cc5f3cafed27d92ce649abeb0939748be373f","observation_id":"60cef787-d628-494d-ad26-17aaade5b57c","resolution":{"observed_at":"2026-05-14T22:48:14.660145Z","resolver_source":"raw_fallback","status":"verified_fuzzy"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}},{"citation":{"cited_paper":null,"cited_work":{"arxiv_id":null,"doi":null,"metadata_source":"raw_reference","pith_arxiv_id":null,"snapshot_observed_at":"2026-06-05T21:23:00.469572Z","title":"Protllm: An interleaved protein-language llm with protein- as-word pre-training","venue":null,"work_id":"753fe614-8fec-4b2f-af88-b8748ef4d5ad","year":2024},"citing_paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","version":2},"reference_index":99,"source":"pdf_text","source_observed_at":"2026-05-14T22:11:30.437422Z"},"links":{"citing_paper":"/paper/2605.10978"},"observation_digest":"sha256:6180715057d6f507db62069aad156e9c8b131e2ed8f52b63f0efd03eb69d7ecb","observation_id":"1a47b4e5-823a-43e3-82af-595741089e22","resolution":{"observed_at":"2026-05-14T22:48:14.481034Z","resolver_source":"raw_fallback","status":"malformed_identifier"},"standing_notice":{"events":[],"observation":"No event found in the named queried sources as of 2026-08-14T06:32:32.682623+00:00.","reason":null,"source_receipts":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"state":"measured"}}],"paper":{"arxiv_id":"2605.10978","last_updated":"2026-05-13T05:15:54Z","latest_version":2,"primary_category":"q-bio.QM","snapshot_observed_at":"2026-08-12T20:32:55.396829Z","submitted_at":"2026-05-09T02:19:38Z","title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design"},"reference_resolution":{"displayed":99,"state_counts":{"malformed_identifier":1,"metadata_mismatch":2,"parse_uncertain":0,"unresolved":3,"verified_exact":19,"verified_fuzzy":74},"total_outbound_references":99},"refusal":"A citation records a reference. It does not transfer a finding from one paper to another.","schema":"pith.paper-citation-record.v1","standing_sources":[{"observed_at":"2026-08-14T06:32:32.682623+00:00","source":"crossref"},{"observed_at":"2026-08-14T06:32:18.44784+00:00","source":"retraction_watch"}],"thesis":"As of 14 August 2026, this Paper Citation Record lists 99 of 99 outbound references and 2 inbound Pith citation observations for arXiv:2605.10978."}