{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2024:UMEPMAHT6YUCUVP5OEKJYBRLXX","short_pith_number":"pith:UMEPMAHT","schema_version":"1.0","canonical_sha256":"a308f600f3f6282a55fd71149c062bbdf231ae3981c3f2df9ef5e8c83e3995ec","source":{"kind":"arxiv","id":"2411.16694","version":1},"attestation_state":"computed","paper":{"title":"Reaction-conditioned De Novo Enzyme Design with GENzyme","license":"http://creativecommons.org/publicdomain/zero/1.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Chenqing Hua, Doina Precup, Guy Wolf, Jian Tang, Jiarui Lu, Odin Zhang, Rex Ying, Shuangjia Zheng, Wengong Jin, Yong Liu","submitted_at":"2024-11-10T00:37:26Z","abstract_excerpt":"The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \\textsc{GENzyme}, a \\textit{de novo} enzyme des"},"verification_status":{"content_addressed":true,"pith_receipt":true,"author_attested":false,"weak_author_claims":0,"strong_author_claims":0,"externally_anchored":false,"storage_verified":false,"citation_signatures":0,"replication_records":0,"graph_snapshot":true,"references_resolved":false,"formal_links_present":false},"canonical_record":{"source":{"id":"2411.16694","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/publicdomain/zero/1.0/","primary_cat":"q-bio.BM","submitted_at":"2024-11-10T00:37:26Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"52090e0a09ca5d62ba21a0b599878910b4d157d1de6510ebc2dea7e5ea8fd357","abstract_canon_sha256":"6627e3a874a91f84fc5dd3eb07335a0aef46a6322ce258bd6f9f828f308bcd35"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:40:22.129985Z","signature_b64":"shrHZ/OJaU78tYB+UHi6JgmLf5AZnN48zzrIa0zmF1gWj63uiBxWbBD5bhGaU+vItVE/70BPhIqIHVBkq/VGBA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"a308f600f3f6282a55fd71149c062bbdf231ae3981c3f2df9ef5e8c83e3995ec","last_reissued_at":"2026-07-05T09:40:22.129485Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:40:22.129485Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Reaction-conditioned De Novo Enzyme Design with GENzyme","license":"http://creativecommons.org/publicdomain/zero/1.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Chenqing Hua, Doina Precup, Guy Wolf, Jian Tang, Jiarui Lu, Odin Zhang, Rex Ying, Shuangjia Zheng, Wengong Jin, Yong Liu","submitted_at":"2024-11-10T00:37:26Z","abstract_excerpt":"The introduction of models like RFDiffusionAA, AlphaFold3, AlphaProteo, and Chai1 has revolutionized protein structure modeling and interaction prediction, primarily from a binding perspective, focusing on creating ideal lock-and-key models. However, these methods can fall short for enzyme-substrate interactions, where perfect binding models are rare, and induced fit states are more common. To address this, we shift to a functional perspective for enzyme design, where the enzyme function is defined by the reaction it catalyzes. Here, we introduce \\textsc{GENzyme}, a \\textit{de novo} enzyme des"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2411.16694","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2411.16694/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"aliases":[{"alias_kind":"arxiv","alias_value":"2411.16694","created_at":"2026-07-05T09:40:22.129542+00:00"},{"alias_kind":"arxiv_version","alias_value":"2411.16694v1","created_at":"2026-07-05T09:40:22.129542+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2411.16694","created_at":"2026-07-05T09:40:22.129542+00:00"},{"alias_kind":"pith_short_12","alias_value":"UMEPMAHT6YUC","created_at":"2026-07-05T09:40:22.129542+00:00"},{"alias_kind":"pith_short_16","alias_value":"UMEPMAHT6YUCUVP5","created_at":"2026-07-05T09:40:22.129542+00:00"},{"alias_kind":"pith_short_8","alias_value":"UMEPMAHT","created_at":"2026-07-05T09:40:22.129542+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":0,"internal_anchor_count":0,"sample":[]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX","json":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX.json","graph_json":"https://pith.science/api/pith-number/UMEPMAHT6YUCUVP5OEKJYBRLXX/graph.json","events_json":"https://pith.science/api/pith-number/UMEPMAHT6YUCUVP5OEKJYBRLXX/events.json","paper":"https://pith.science/paper/UMEPMAHT"},"agent_actions":{"view_html":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX","download_json":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX.json","view_paper":"https://pith.science/paper/UMEPMAHT","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2411.16694&json=true","fetch_graph":"https://pith.science/api/pith-number/UMEPMAHT6YUCUVP5OEKJYBRLXX/graph.json","fetch_events":"https://pith.science/api/pith-number/UMEPMAHT6YUCUVP5OEKJYBRLXX/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX/action/timestamp_anchor","attest_storage":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX/action/storage_attestation","attest_author":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX/action/author_attestation","sign_citation":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX/action/citation_signature","submit_replication":"https://pith.science/pith/UMEPMAHT6YUCUVP5OEKJYBRLXX/action/replication_record"}},"created_at":"2026-07-05T09:40:22.129542+00:00","updated_at":"2026-07-05T09:40:22.129542+00:00"}