{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2025:FP477FVJC3ZO5L2JMCPOFBFEPD","short_pith_number":"pith:FP477FVJ","canonical_record":{"source":{"id":"2507.14156","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-07-04T11:57:38Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"5c17487532fa56ae317b998677b3d5f177377c0f407cd0c3c7494714d0cbab55","abstract_canon_sha256":"dd7b3fb779d8418d3c44c178624e3ca02d782e4d4b2f726f35e6637e850c1b7d"},"schema_version":"1.0"},"canonical_sha256":"2bf9ff96a916f2eeaf49609ee284a478d5f6c7eb8e4c066937529c12d6048a1f","source":{"kind":"arxiv","id":"2507.14156","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2507.14156","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"arxiv_version","alias_value":"2507.14156v1","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2507.14156","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_12","alias_value":"FP477FVJC3ZO","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_16","alias_value":"FP477FVJC3ZO5L2J","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_8","alias_value":"FP477FVJ","created_at":"2026-07-05T11:39:29Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2025:FP477FVJC3ZO5L2JMCPOFBFEPD","target":"record","payload":{"canonical_record":{"source":{"id":"2507.14156","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-07-04T11:57:38Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"5c17487532fa56ae317b998677b3d5f177377c0f407cd0c3c7494714d0cbab55","abstract_canon_sha256":"dd7b3fb779d8418d3c44c178624e3ca02d782e4d4b2f726f35e6637e850c1b7d"},"schema_version":"1.0"},"canonical_sha256":"2bf9ff96a916f2eeaf49609ee284a478d5f6c7eb8e4c066937529c12d6048a1f","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T11:39:29.778435Z","signature_b64":"kLjDo3WKmtxwca+n35xMdJy6dV9Xkqey1ZYp/hjV77VEsy5aO1b5u7+QO1O1QOpomWsJK/c8W4YPcytM0o5PDA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"2bf9ff96a916f2eeaf49609ee284a478d5f6c7eb8e4c066937529c12d6048a1f","last_reissued_at":"2026-07-05T11:39:29.777978Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T11:39:29.777978Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2507.14156","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":"2026-07-05T11:39:29Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"GR7pgyYa4hLQwrkmAQlu+ZuRUaULuaYluO/CZ0Git7RhGxAJA1YbKqlrHowC5LnV6Jlx5SVSVwUTI7Mgf9qxAg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T11:00:42.021607Z"},"content_sha256":"e130ae9d45438100e630ce6faa38a7eb66dd1f43b80eaffc8e2ef02035a83b45","schema_version":"1.0","event_id":"sha256:e130ae9d45438100e630ce6faa38a7eb66dd1f43b80eaffc8e2ef02035a83b45"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2025:FP477FVJC3ZO5L2JMCPOFBFEPD","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"All-atom inverse protein folding through discrete flow matching","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Kai Yi, Kiarash Jamali, Sjors H. W. Scheres","submitted_at":"2025-07-04T11:57:38Z","abstract_excerpt":"The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein folding, the objective is to find a sequence of amino acids that adopts a target protein structure. Many inverse folding methods struggle to predict sequences for complexes that contain non-protein components, and perform poorly with complexes that adopt multiple structural states. To address these challenges, we present ADFLIP (All-atom Discrete FLow matching Inv"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2507.14156","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/2507.14156/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":"2026-07-05T11:39:29Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"euOQ8GvEmOAwRQ8x4GcxM4S90azpa8gfP2JJoKGm8ovR2WdXbbSiGYD2L2vteHYMkCnVGQVcTRth+uBXDvUFCQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-08T11:00:42.022139Z"},"content_sha256":"83dd7cbc41d039beed0aebb46b6f1eac3915dc5e1b47cdb651eeff6ffeab6760","schema_version":"1.0","event_id":"sha256:83dd7cbc41d039beed0aebb46b6f1eac3915dc5e1b47cdb651eeff6ffeab6760"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/bundle.json","state_url":"https://pith.science/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/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":"2026-08-08T11:00:42Z","links":{"resolver":"https://pith.science/pith/FP477FVJC3ZO5L2JMCPOFBFEPD","bundle":"https://pith.science/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/bundle.json","state":"https://pith.science/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/state.json","well_known_bundle":"https://pith.science/.well-known/pith/FP477FVJC3ZO5L2JMCPOFBFEPD/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2025:FP477FVJC3ZO5L2JMCPOFBFEPD","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":"dd7b3fb779d8418d3c44c178624e3ca02d782e4d4b2f726f35e6637e850c1b7d","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-07-04T11:57:38Z","title_canon_sha256":"5c17487532fa56ae317b998677b3d5f177377c0f407cd0c3c7494714d0cbab55"},"schema_version":"1.0","source":{"id":"2507.14156","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2507.14156","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"arxiv_version","alias_value":"2507.14156v1","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2507.14156","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_12","alias_value":"FP477FVJC3ZO","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_16","alias_value":"FP477FVJC3ZO5L2J","created_at":"2026-07-05T11:39:29Z"},{"alias_kind":"pith_short_8","alias_value":"FP477FVJ","created_at":"2026-07-05T11:39:29Z"}],"graph_snapshots":[{"event_id":"sha256:83dd7cbc41d039beed0aebb46b6f1eac3915dc5e1b47cdb651eeff6ffeab6760","target":"graph","created_at":"2026-07-05T11:39:29Z","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/2507.14156/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein folding, the objective is to find a sequence of amino acids that adopts a target protein structure. Many inverse folding methods struggle to predict sequences for complexes that contain non-protein components, and perform poorly with complexes that adopt multiple structural states. To address these challenges, we present ADFLIP (All-atom Discrete FLow matching Inv","authors_text":"Kai Yi, Kiarash Jamali, Sjors H. W. Scheres","cross_cats":["cs.AI"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-07-04T11:57:38Z","title":"All-atom inverse protein folding through discrete flow matching"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2507.14156","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:e130ae9d45438100e630ce6faa38a7eb66dd1f43b80eaffc8e2ef02035a83b45","target":"record","created_at":"2026-07-05T11:39:29Z","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":"dd7b3fb779d8418d3c44c178624e3ca02d782e4d4b2f726f35e6637e850c1b7d","cross_cats_sorted":["cs.AI"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2025-07-04T11:57:38Z","title_canon_sha256":"5c17487532fa56ae317b998677b3d5f177377c0f407cd0c3c7494714d0cbab55"},"schema_version":"1.0","source":{"id":"2507.14156","kind":"arxiv","version":1}},"canonical_sha256":"2bf9ff96a916f2eeaf49609ee284a478d5f6c7eb8e4c066937529c12d6048a1f","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"2bf9ff96a916f2eeaf49609ee284a478d5f6c7eb8e4c066937529c12d6048a1f","first_computed_at":"2026-07-05T11:39:29.777978Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T11:39:29.777978Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"kLjDo3WKmtxwca+n35xMdJy6dV9Xkqey1ZYp/hjV77VEsy5aO1b5u7+QO1O1QOpomWsJK/c8W4YPcytM0o5PDA==","signature_status":"signed_v1","signed_at":"2026-07-05T11:39:29.778435Z","signed_message":"canonical_sha256_bytes"},"source_id":"2507.14156","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:e130ae9d45438100e630ce6faa38a7eb66dd1f43b80eaffc8e2ef02035a83b45","sha256:83dd7cbc41d039beed0aebb46b6f1eac3915dc5e1b47cdb651eeff6ffeab6760"],"state_sha256":"9a7f6250dccd005171dffbe03de85532e41d260166257d6d15a953a2d1828c4f"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"bw64e4effs4k16KyGknCMSIibGRGtDhRzretASgNZu1o1pdGTNS3Hzi7NyKcuyOmNJufc/F6EMCIMdRqmw7SDg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-08T11:00:42.027340Z","bundle_sha256":"c9a84546a19b321b59b536a83fd36ba2799ede63e6d987fb49c6c684af963c6c"}}