{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:NKW5R75AMNAPDP47MUFZORKKVN","short_pith_number":"pith:NKW5R75A","canonical_record":{"source":{"id":"2405.03370","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-05-06T11:23:47Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"d1ec213d4ca53adc8f9a922c64c82a195d48239563c6d0a3a2ee07daf177a0a9","abstract_canon_sha256":"62e83770b18aade67a7a20778de518f1a4844d0bff42e4f116a580eabbc7eb33"},"schema_version":"1.0"},"canonical_sha256":"6aadd8ffa06340f1bf9f650b97454aab600511c2d0dffaa2cf8ee148d1f084b0","source":{"kind":"arxiv","id":"2405.03370","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2405.03370","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"arxiv_version","alias_value":"2405.03370v1","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2405.03370","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_12","alias_value":"NKW5R75AMNAP","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_16","alias_value":"NKW5R75AMNAPDP47","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_8","alias_value":"NKW5R75A","created_at":"2026-07-05T08:16:02Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:NKW5R75AMNAPDP47MUFZORKKVN","target":"record","payload":{"canonical_record":{"source":{"id":"2405.03370","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-05-06T11:23:47Z","cross_cats_sorted":["q-bio.QM"],"title_canon_sha256":"d1ec213d4ca53adc8f9a922c64c82a195d48239563c6d0a3a2ee07daf177a0a9","abstract_canon_sha256":"62e83770b18aade67a7a20778de518f1a4844d0bff42e4f116a580eabbc7eb33"},"schema_version":"1.0"},"canonical_sha256":"6aadd8ffa06340f1bf9f650b97454aab600511c2d0dffaa2cf8ee148d1f084b0","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T08:16:02.146743Z","signature_b64":"zriqDGYLijT09kyJQgIPIBkXz57Ee6O0AXWsvP8SzQhgxIITPnf2ImGoSotGrcyyAiIYFz5hHgSZmXu+42SRDQ==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"6aadd8ffa06340f1bf9f650b97454aab600511c2d0dffaa2cf8ee148d1f084b0","last_reissued_at":"2026-07-05T08:16:02.146347Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T08:16:02.146347Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2405.03370","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":"2026-07-05T08:16:02Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"+gHNSHLHlsrXG6yOK5SYMGl+JYjM9o02P5suzIYHKJm1a5o8r1ur7Lxrmp+xy52wqtYHZwbpXKsgGxSXVg1SBA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T17:04:24.460416Z"},"content_sha256":"a8642ce08e7a15062386142921a3708123c0790ffb7b852a13f8f059c2d3eeab","schema_version":"1.0","event_id":"sha256:a8642ce08e7a15062386142921a3708123c0790ffb7b852a13f8f059c2d3eeab"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:NKW5R75AMNAPDP47MUFZORKKVN","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"AntiFold: Improved antibody structure-based design using inverse folding","license":"http://creativecommons.org/licenses/by-sa/4.0/","headline":"","cross_cats":["q-bio.QM"],"primary_cat":"q-bio.BM","authors_text":"Alissa Hummer, Broncio Aguilar-Sanjuan, Charlotte M. Deane, Magnus Haraldson H{\\o}ie, Morten Nielsen, Tobias H. Olsen","submitted_at":"2024-05-06T11:23:47Z","abstract_excerpt":"The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining structural integrity during antibody design. Here, we present AntiFold, an antibody-specific inverse folding model, fine-tuned from ESM-IF1 on solved and predicted antibody structures. AntiFold outperforms existing inverse folding tools on sequence recovery across complementarity-determining regions, with designed sequences showing high structural similarit"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2405.03370","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/2405.03370/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":"2026-07-05T08:16:02Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"pIxHAsDR3/b+JKntL78FTi5K5Cg5WqSytWen+MhrFGV/glCOr9kTIiGbDtOkR3I32FuFAcFNRcRZZDlASffgDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T17:04:24.460922Z"},"content_sha256":"82889614555b244bc53a65dc63d599c151d61c9a4d4101db7881bfebda8de4f8","schema_version":"1.0","event_id":"sha256:82889614555b244bc53a65dc63d599c151d61c9a4d4101db7881bfebda8de4f8"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/NKW5R75AMNAPDP47MUFZORKKVN/bundle.json","state_url":"https://pith.science/pith/NKW5R75AMNAPDP47MUFZORKKVN/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/NKW5R75AMNAPDP47MUFZORKKVN/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":"2026-08-04T17:04:24Z","links":{"resolver":"https://pith.science/pith/NKW5R75AMNAPDP47MUFZORKKVN","bundle":"https://pith.science/pith/NKW5R75AMNAPDP47MUFZORKKVN/bundle.json","state":"https://pith.science/pith/NKW5R75AMNAPDP47MUFZORKKVN/state.json","well_known_bundle":"https://pith.science/.well-known/pith/NKW5R75AMNAPDP47MUFZORKKVN/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:NKW5R75AMNAPDP47MUFZORKKVN","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":"62e83770b18aade67a7a20778de518f1a4844d0bff42e4f116a580eabbc7eb33","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-05-06T11:23:47Z","title_canon_sha256":"d1ec213d4ca53adc8f9a922c64c82a195d48239563c6d0a3a2ee07daf177a0a9"},"schema_version":"1.0","source":{"id":"2405.03370","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2405.03370","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"arxiv_version","alias_value":"2405.03370v1","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2405.03370","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_12","alias_value":"NKW5R75AMNAP","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_16","alias_value":"NKW5R75AMNAPDP47","created_at":"2026-07-05T08:16:02Z"},{"alias_kind":"pith_short_8","alias_value":"NKW5R75A","created_at":"2026-07-05T08:16:02Z"}],"graph_snapshots":[{"event_id":"sha256:82889614555b244bc53a65dc63d599c151d61c9a4d4101db7881bfebda8de4f8","target":"graph","created_at":"2026-07-05T08:16:02Z","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/2405.03370/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"The design and optimization of antibodies requires an intricate balance across multiple properties. Protein inverse folding models, capable of generating diverse sequences folding into the same structure, are promising tools for maintaining structural integrity during antibody design. Here, we present AntiFold, an antibody-specific inverse folding model, fine-tuned from ESM-IF1 on solved and predicted antibody structures. AntiFold outperforms existing inverse folding tools on sequence recovery across complementarity-determining regions, with designed sequences showing high structural similarit","authors_text":"Alissa Hummer, Broncio Aguilar-Sanjuan, Charlotte M. Deane, Magnus Haraldson H{\\o}ie, Morten Nielsen, Tobias H. Olsen","cross_cats":["q-bio.QM"],"headline":"","license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-05-06T11:23:47Z","title":"AntiFold: Improved antibody structure-based design using inverse folding"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2405.03370","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:a8642ce08e7a15062386142921a3708123c0790ffb7b852a13f8f059c2d3eeab","target":"record","created_at":"2026-07-05T08:16:02Z","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":"62e83770b18aade67a7a20778de518f1a4844d0bff42e4f116a580eabbc7eb33","cross_cats_sorted":["q-bio.QM"],"license":"http://creativecommons.org/licenses/by-sa/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-05-06T11:23:47Z","title_canon_sha256":"d1ec213d4ca53adc8f9a922c64c82a195d48239563c6d0a3a2ee07daf177a0a9"},"schema_version":"1.0","source":{"id":"2405.03370","kind":"arxiv","version":1}},"canonical_sha256":"6aadd8ffa06340f1bf9f650b97454aab600511c2d0dffaa2cf8ee148d1f084b0","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"6aadd8ffa06340f1bf9f650b97454aab600511c2d0dffaa2cf8ee148d1f084b0","first_computed_at":"2026-07-05T08:16:02.146347Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T08:16:02.146347Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"zriqDGYLijT09kyJQgIPIBkXz57Ee6O0AXWsvP8SzQhgxIITPnf2ImGoSotGrcyyAiIYFz5hHgSZmXu+42SRDQ==","signature_status":"signed_v1","signed_at":"2026-07-05T08:16:02.146743Z","signed_message":"canonical_sha256_bytes"},"source_id":"2405.03370","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:a8642ce08e7a15062386142921a3708123c0790ffb7b852a13f8f059c2d3eeab","sha256:82889614555b244bc53a65dc63d599c151d61c9a4d4101db7881bfebda8de4f8"],"state_sha256":"b0d16a99bf3c805724f151095b28c638842eff5bb0f9b23279b0f267cb5ce2bc"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"++NRRDNRVG6CfnYPneUJX5rPMilJVdOWcIuRLVk0HEdc6R4ikOD+wTRjyMJqd9Ijktgj8OzoiCA/MCiiLARcDQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T17:04:24.464666Z","bundle_sha256":"9690ac669fc3b947815443b7f888f9409f1f083fedc06b95922d8a821d13abf7"}}