{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2024:YSRIHTGWBZROEDD52JWSGKBX4A","short_pith_number":"pith:YSRIHTGW","schema_version":"1.0","canonical_sha256":"c4a283ccd60e62e20c7dd26d232837e001cbdc1c6986c8a198a29b440ebe8fe5","source":{"kind":"arxiv","id":"2406.03979","version":1},"attestation_state":"computed","paper":{"title":"Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["math.AT","q-bio.QM"],"primary_cat":"q-bio.BM","authors_text":"Guo-Wei Wei, JunJie Wee","submitted_at":"2024-06-06T11:45:36Z","abstract_excerpt":"AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step towards comprehensive, automated protein structure prediction. However, independent validation of AF3's predictions is necessary. Evaluated using the SKEMPI 2.0 database which involves 317 protein-protein complexes and 8338 mutations, AF3 complex structures give rise to a very good Pearson correlation coefficient of 0.86 for predicting protein-protein binding free"},"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":"2406.03979","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-06-06T11:45:36Z","cross_cats_sorted":["math.AT","q-bio.QM"],"title_canon_sha256":"fa24f635d879f3ad7b24780b66c79173f2dab1765119ec47c3442640cd5cbad2","abstract_canon_sha256":"ef98a207a2f263d126a691a62910486c01fc46933acd425f047281d12a962e30"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T08:28:18.635214Z","signature_b64":"Qlr9rGJdcZ6TnS0mkpuDc59gJd80yzfXuYFO9j+/XDZbPOkabbo7bQiFsZJlnvPnQPFl5ZuIZlaoS/nVU6M5AA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"c4a283ccd60e62e20c7dd26d232837e001cbdc1c6986c8a198a29b440ebe8fe5","last_reissued_at":"2026-07-05T08:28:18.634759Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T08:28:18.634759Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Benchmarking AlphaFold3's protein-protein complex accuracy and machine learning prediction reliability for binding free energy changes upon mutation","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["math.AT","q-bio.QM"],"primary_cat":"q-bio.BM","authors_text":"Guo-Wei Wei, JunJie Wee","submitted_at":"2024-06-06T11:45:36Z","abstract_excerpt":"AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step towards comprehensive, automated protein structure prediction. However, independent validation of AF3's predictions is necessary. Evaluated using the SKEMPI 2.0 database which involves 317 protein-protein complexes and 8338 mutations, AF3 complex structures give rise to a very good Pearson correlation coefficient of 0.86 for predicting protein-protein binding free"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2406.03979","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/2406.03979/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":"2406.03979","created_at":"2026-07-05T08:28:18.634815+00:00"},{"alias_kind":"arxiv_version","alias_value":"2406.03979v1","created_at":"2026-07-05T08:28:18.634815+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2406.03979","created_at":"2026-07-05T08:28:18.634815+00:00"},{"alias_kind":"pith_short_12","alias_value":"YSRIHTGWBZRO","created_at":"2026-07-05T08:28:18.634815+00:00"},{"alias_kind":"pith_short_16","alias_value":"YSRIHTGWBZROEDD5","created_at":"2026-07-05T08:28:18.634815+00:00"},{"alias_kind":"pith_short_8","alias_value":"YSRIHTGW","created_at":"2026-07-05T08:28:18.634815+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/YSRIHTGWBZROEDD52JWSGKBX4A","json":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A.json","graph_json":"https://pith.science/api/pith-number/YSRIHTGWBZROEDD52JWSGKBX4A/graph.json","events_json":"https://pith.science/api/pith-number/YSRIHTGWBZROEDD52JWSGKBX4A/events.json","paper":"https://pith.science/paper/YSRIHTGW"},"agent_actions":{"view_html":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A","download_json":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A.json","view_paper":"https://pith.science/paper/YSRIHTGW","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2406.03979&json=true","fetch_graph":"https://pith.science/api/pith-number/YSRIHTGWBZROEDD52JWSGKBX4A/graph.json","fetch_events":"https://pith.science/api/pith-number/YSRIHTGWBZROEDD52JWSGKBX4A/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A/action/timestamp_anchor","attest_storage":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A/action/storage_attestation","attest_author":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A/action/author_attestation","sign_citation":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A/action/citation_signature","submit_replication":"https://pith.science/pith/YSRIHTGWBZROEDD52JWSGKBX4A/action/replication_record"}},"created_at":"2026-07-05T08:28:18.634815+00:00","updated_at":"2026-07-05T08:28:18.634815+00:00"}