{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:ZYNNW6TIU276M72773MV5V2GK4","short_pith_number":"pith:ZYNNW6TI","canonical_record":{"source":{"id":"2503.03989","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-06T00:34:44Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"aaf3e419cbdf2d87b3e627ffd3b33ec18e44f94416669d7bae3dc434bb7ae5a6","abstract_canon_sha256":"7fa21d16f7ee6c350a065b08ad3a64b5e0ce077b29473f770eb5071f408a56e0"},"schema_version":"1.0"},"canonical_sha256":"ce1adb7a68a6bfe67f5ffed95ed746570767f15656e7a2e86bd682c14bf996af","source":{"kind":"arxiv","id":"2503.03989","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2503.03989","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"arxiv_version","alias_value":"2503.03989v1","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2503.03989","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_12","alias_value":"ZYNNW6TIU276","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_16","alias_value":"ZYNNW6TIU276M727","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_8","alias_value":"ZYNNW6TI","created_at":"2026-07-05T10:25:26Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:ZYNNW6TIU276M72773MV5V2GK4","target":"record","payload":{"canonical_record":{"source":{"id":"2503.03989","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-06T00:34:44Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"aaf3e419cbdf2d87b3e627ffd3b33ec18e44f94416669d7bae3dc434bb7ae5a6","abstract_canon_sha256":"7fa21d16f7ee6c350a065b08ad3a64b5e0ce077b29473f770eb5071f408a56e0"},"schema_version":"1.0"},"canonical_sha256":"ce1adb7a68a6bfe67f5ffed95ed746570767f15656e7a2e86bd682c14bf996af","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:25:26.044555Z","signature_b64":"NJ9mxKEtfKXcUTpsR8oFp2c+ofYipLMYinR9OfkTqDJXoP/4ZJTdS0bluTDxkbUE2szvZTEEnpaKXYVlv9IODw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"ce1adb7a68a6bfe67f5ffed95ed746570767f15656e7a2e86bd682c14bf996af","last_reissued_at":"2026-07-05T10:25:26.043502Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:25:26.043502Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2503.03989","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T10:25:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"AGOigDf1aJbiRNBVzlE1EK8ZK/a/IyAUrpRxSnsrJc66Fk6spf3g+GbWv/G95bT0gxhhjgeVLbER+Va/Ip/BCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-22T06:09:58.676708Z"},"content_sha256":"3115ec1265b4edb32027b7c8d7da978bb5bbb213bff7831244803a7bc66ee48b","schema_version":"1.0","event_id":"sha256:3115ec1265b4edb32027b7c8d7da978bb5bbb213bff7831244803a7bc66ee48b"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:ZYNNW6TIU276M72773MV5V2GK4","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.BM","authors_text":"Feng Zhou, Haowei Lin, Jianzhu Ma, Jiaqi Guan, Liang Wang, Qiang Liu, Xiangxin Zhou, Xinheng He, Yang Wang, Yi Xiao","submitted_at":"2025-03-06T00:34:44Z","abstract_excerpt":"The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2503.03989","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/2503.03989/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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T10:25:26Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"zgJNOEMhY64C9r9KL//bBRdeRK89QuJd5qsQV8g93gKGSynqA7F7XBH1mWZs0/L8ygldTeEiPq2coFUz1WomCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-22T06:09:58.677347Z"},"content_sha256":"8b8dece01be7f4d69a37e854628524482f7278fc9b4c794108639ce6869be40f","schema_version":"1.0","event_id":"sha256:8b8dece01be7f4d69a37e854628524482f7278fc9b4c794108639ce6869be40f"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/ZYNNW6TIU276M72773MV5V2GK4/bundle.json","state_url":"https://pith.science/pith/ZYNNW6TIU276M72773MV5V2GK4/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/ZYNNW6TIU276M72773MV5V2GK4/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-08-22T06:09:58Z","links":{"resolver":"https://pith.science/pith/ZYNNW6TIU276M72773MV5V2GK4","bundle":"https://pith.science/pith/ZYNNW6TIU276M72773MV5V2GK4/bundle.json","state":"https://pith.science/pith/ZYNNW6TIU276M72773MV5V2GK4/state.json","well_known_bundle":"https://pith.science/.well-known/pith/ZYNNW6TIU276M72773MV5V2GK4/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:ZYNNW6TIU276M72773MV5V2GK4","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"7fa21d16f7ee6c350a065b08ad3a64b5e0ce077b29473f770eb5071f408a56e0","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-06T00:34:44Z","title_canon_sha256":"aaf3e419cbdf2d87b3e627ffd3b33ec18e44f94416669d7bae3dc434bb7ae5a6"},"schema_version":"1.0","source":{"id":"2503.03989","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2503.03989","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"arxiv_version","alias_value":"2503.03989v1","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2503.03989","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_12","alias_value":"ZYNNW6TIU276","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_16","alias_value":"ZYNNW6TIU276M727","created_at":"2026-07-05T10:25:26Z"},{"alias_kind":"pith_short_8","alias_value":"ZYNNW6TI","created_at":"2026-07-05T10:25:26Z"}],"graph_snapshots":[{"event_id":"sha256:8b8dece01be7f4d69a37e854628524482f7278fc9b4c794108639ce6869be40f","target":"graph","created_at":"2026-07-05T10:25:26Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2503.03989/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, ","authors_text":"Feng Zhou, Haowei Lin, Jianzhu Ma, Jiaqi Guan, Liang Wang, Qiang Liu, Xiangxin Zhou, Xinheng He, Yang Wang, Yi Xiao","cross_cats":["cs.LG"],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-06T00:34:44Z","title":"Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2503.03989","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:3115ec1265b4edb32027b7c8d7da978bb5bbb213bff7831244803a7bc66ee48b","target":"record","created_at":"2026-07-05T10:25:26Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"7fa21d16f7ee6c350a065b08ad3a64b5e0ce077b29473f770eb5071f408a56e0","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-03-06T00:34:44Z","title_canon_sha256":"aaf3e419cbdf2d87b3e627ffd3b33ec18e44f94416669d7bae3dc434bb7ae5a6"},"schema_version":"1.0","source":{"id":"2503.03989","kind":"arxiv","version":1}},"canonical_sha256":"ce1adb7a68a6bfe67f5ffed95ed746570767f15656e7a2e86bd682c14bf996af","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"ce1adb7a68a6bfe67f5ffed95ed746570767f15656e7a2e86bd682c14bf996af","first_computed_at":"2026-07-05T10:25:26.043502Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:25:26.043502Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"NJ9mxKEtfKXcUTpsR8oFp2c+ofYipLMYinR9OfkTqDJXoP/4ZJTdS0bluTDxkbUE2szvZTEEnpaKXYVlv9IODw==","signature_status":"signed_v1","signed_at":"2026-07-05T10:25:26.044555Z","signed_message":"canonical_sha256_bytes"},"source_id":"2503.03989","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:3115ec1265b4edb32027b7c8d7da978bb5bbb213bff7831244803a7bc66ee48b","sha256:8b8dece01be7f4d69a37e854628524482f7278fc9b4c794108639ce6869be40f"],"state_sha256":"44ab390894c4883fadd7863c6403ca1c7be0e0a293b50acc7985d478a8a5f0e0"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"v5Fpt3I1s7Ev6lBJCDQgilmuaclz9MtXsJBkXNeHwodTQ/VvRxvmbRUI8UWM0jeDZAmFhVFCF/s7s5iNNtt4AQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-22T06:09:58.682438Z","bundle_sha256":"19a552f1b7a537bd63eb68b94d0876762f221a6b0d2c21c106d02f4d7049da88"}}