{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:LRPBZFEXGXU2SMB74F64ILFGYC","short_pith_number":"pith:LRPBZFEX","canonical_record":{"source":{"id":"2503.00165","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-28T20:27:14Z","cross_cats_sorted":[],"title_canon_sha256":"1fb824e1eaf7e6443c9e9347f424eef4e1c22be1ff4147cf0e36a337208598bf","abstract_canon_sha256":"6959ca977402237c256955458d2bbc87e1123f08b3d5d81b4f94fa40afa130bb"},"schema_version":"1.0"},"canonical_sha256":"5c5e1c949735e9a9303fe17dc42ca6c0ab9a104b1d742ffdedf0c3e497a5e808","source":{"kind":"arxiv","id":"2503.00165","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2503.00165","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"arxiv_version","alias_value":"2503.00165v1","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2503.00165","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_12","alias_value":"LRPBZFEXGXU2","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_16","alias_value":"LRPBZFEXGXU2SMB7","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_8","alias_value":"LRPBZFEX","created_at":"2026-07-05T10:22:18Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:LRPBZFEXGXU2SMB74F64ILFGYC","target":"record","payload":{"canonical_record":{"source":{"id":"2503.00165","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-28T20:27:14Z","cross_cats_sorted":[],"title_canon_sha256":"1fb824e1eaf7e6443c9e9347f424eef4e1c22be1ff4147cf0e36a337208598bf","abstract_canon_sha256":"6959ca977402237c256955458d2bbc87e1123f08b3d5d81b4f94fa40afa130bb"},"schema_version":"1.0"},"canonical_sha256":"5c5e1c949735e9a9303fe17dc42ca6c0ab9a104b1d742ffdedf0c3e497a5e808","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:22:18.397342Z","signature_b64":"XCWLVf6KCH9eRIMtZUNgEbAqzmswJjEJcS85HSvl+QonqJ92Kt1ze66fqvMIhL62R0Wc2qNFyf+bP617PPN4BQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"5c5e1c949735e9a9303fe17dc42ca6c0ab9a104b1d742ffdedf0c3e497a5e808","last_reissued_at":"2026-07-05T10:22:18.396836Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:22:18.396836Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2503.00165","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":"2026-07-05T10:22:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"/n+r3Yl7L7IoSeWR+i1yv9TWLDrUU9hEJfQ+/Bv1Uopzv5eMma6GzbBAx3M72n418ZrnikSUaaqebIzi5Bj5Aw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T09:19:36.136728Z"},"content_sha256":"4ff864868a5580e4c32a94167ecc117fa875796a18190000ae3a454c0f96ed9c","schema_version":"1.0","event_id":"sha256:4ff864868a5580e4c32a94167ecc117fa875796a18190000ae3a454c0f96ed9c"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:LRPBZFEXGXU2SMB74F64ILFGYC","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.BM","authors_text":"Enming Xing, Junjie Zhang, Shen Wang, Xiaolin Cheng","submitted_at":"2025-02-28T20:27:14Z","abstract_excerpt":"AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static structural information, but also hold critical details about protein dynamics, which underpin biological functions. However, these subtle co-evolutionary signatures, which dictate conformational state preferences, are often obscured by noise within MSA data and thus remain challenging to decipher. Here, we introduce AF-ClaSeq, a systematic framework that isolates these co-evolutionary signals through sequence purifi"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2503.00165","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/2503.00165/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":"2026-07-05T10:22:18Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"4zruONo/pzknLWd3FU8jW6MQINH86PtEKxVG7ByH/iHJ9Y9tm2RtFQiFj3IcEblkR9mq4TCxhUDkkvI01Y2nAA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T09:19:36.137221Z"},"content_sha256":"87203b83edf436369c483ebd272d52a8b69f733a5e55be9d24ac4c25a2a74351","schema_version":"1.0","event_id":"sha256:87203b83edf436369c483ebd272d52a8b69f733a5e55be9d24ac4c25a2a74351"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/LRPBZFEXGXU2SMB74F64ILFGYC/bundle.json","state_url":"https://pith.science/pith/LRPBZFEXGXU2SMB74F64ILFGYC/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/LRPBZFEXGXU2SMB74F64ILFGYC/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":"2026-08-08T09:19:36Z","links":{"resolver":"https://pith.science/pith/LRPBZFEXGXU2SMB74F64ILFGYC","bundle":"https://pith.science/pith/LRPBZFEXGXU2SMB74F64ILFGYC/bundle.json","state":"https://pith.science/pith/LRPBZFEXGXU2SMB74F64ILFGYC/state.json","well_known_bundle":"https://pith.science/.well-known/pith/LRPBZFEXGXU2SMB74F64ILFGYC/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:LRPBZFEXGXU2SMB74F64ILFGYC","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":"6959ca977402237c256955458d2bbc87e1123f08b3d5d81b4f94fa40afa130bb","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-28T20:27:14Z","title_canon_sha256":"1fb824e1eaf7e6443c9e9347f424eef4e1c22be1ff4147cf0e36a337208598bf"},"schema_version":"1.0","source":{"id":"2503.00165","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2503.00165","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"arxiv_version","alias_value":"2503.00165v1","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2503.00165","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_12","alias_value":"LRPBZFEXGXU2","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_16","alias_value":"LRPBZFEXGXU2SMB7","created_at":"2026-07-05T10:22:18Z"},{"alias_kind":"pith_short_8","alias_value":"LRPBZFEX","created_at":"2026-07-05T10:22:18Z"}],"graph_snapshots":[{"event_id":"sha256:87203b83edf436369c483ebd272d52a8b69f733a5e55be9d24ac4c25a2a74351","target":"graph","created_at":"2026-07-05T10:22:18Z","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/2503.00165/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static structural information, but also hold critical details about protein dynamics, which underpin biological functions. However, these subtle co-evolutionary signatures, which dictate conformational state preferences, are often obscured by noise within MSA data and thus remain challenging to decipher. Here, we introduce AF-ClaSeq, a systematic framework that isolates these co-evolutionary signals through sequence purifi","authors_text":"Enming Xing, Junjie Zhang, Shen Wang, Xiaolin Cheng","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-28T20:27:14Z","title":"Leveraging Sequence Purification for Accurate Prediction of Multiple Conformational States with AlphaFold2"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2503.00165","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":"sha256:4ff864868a5580e4c32a94167ecc117fa875796a18190000ae3a454c0f96ed9c","target":"record","created_at":"2026-07-05T10:22:18Z","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":"6959ca977402237c256955458d2bbc87e1123f08b3d5d81b4f94fa40afa130bb","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-02-28T20:27:14Z","title_canon_sha256":"1fb824e1eaf7e6443c9e9347f424eef4e1c22be1ff4147cf0e36a337208598bf"},"schema_version":"1.0","source":{"id":"2503.00165","kind":"arxiv","version":1}},"canonical_sha256":"5c5e1c949735e9a9303fe17dc42ca6c0ab9a104b1d742ffdedf0c3e497a5e808","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"5c5e1c949735e9a9303fe17dc42ca6c0ab9a104b1d742ffdedf0c3e497a5e808","first_computed_at":"2026-07-05T10:22:18.396836Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:22:18.396836Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"XCWLVf6KCH9eRIMtZUNgEbAqzmswJjEJcS85HSvl+QonqJ92Kt1ze66fqvMIhL62R0Wc2qNFyf+bP617PPN4BQ==","signature_status":"signed_v1","signed_at":"2026-07-05T10:22:18.397342Z","signed_message":"canonical_sha256_bytes"},"source_id":"2503.00165","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:4ff864868a5580e4c32a94167ecc117fa875796a18190000ae3a454c0f96ed9c","sha256:87203b83edf436369c483ebd272d52a8b69f733a5e55be9d24ac4c25a2a74351"],"state_sha256":"03b751110000e92db5114274ce1311d644a2cec6bc0d9c519380bf1aff1e8705"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"sXGaez933tn7RIT00Cb2qbBiSlXvTtIvVC2vKYBNXVDzuml2W0gZ2jqcucMwpufBNKeAYu4oBPP/DV9Sp564Dw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-08T09:19:36.141094Z","bundle_sha256":"b10f0df68c75c25bc3b793c1212f3b21ea149c2f3c7ebfdf4ef63cf651b854ba"}}