{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2024:TXW3QHWZYPBPSIUGYLZLUNNXRC","short_pith_number":"pith:TXW3QHWZ","schema_version":"1.0","canonical_sha256":"9dedb81ed9c3c2f92286c2f2ba35b788b8ddd4fb12e15d554cdc0d39e03c1037","source":{"kind":"arxiv","id":"2406.09586","version":3},"attestation_state":"computed","paper":{"title":"Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.BM","authors_text":"Rex Ying, Tinglin Huang, Wengong Jin, Zhenqiao Song","submitted_at":"2024-06-13T20:46:51Z","abstract_excerpt":"Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to learn protein-aptamer binding. To this end, we develop an unsupervised learning approach based on the predicted pairwise contact map between a protein and a nucleic acid and demonstrate its effectiveness in protein-aptamer binding prediction. Our model is based on FAFormer, a novel equivariant transformer architecture that seamlessly integrates frame averag"},"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":"2406.09586","kind":"arxiv","version":3},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-06-13T20:46:51Z","cross_cats_sorted":[],"title_canon_sha256":"979b1a2c01041312b55f09514bd287c17f0e7c8e5d3320d5373bffbbc22ed88c","abstract_canon_sha256":"f2f162926766a71239b348d649acf3f7c21b01101ca7f56eff9372ab7e110857"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T09:30:17.106201Z","signature_b64":"MzOIXavmvBlfGc0lpI+MmSi07S+o9nff4S4J9OhSpjqlq/EPGE0KdcW5kUIkKs66A15S8nwoa96qHaKrBFPNDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"9dedb81ed9c3c2f92286c2f2ba35b788b8ddd4fb12e15d554cdc0d39e03c1037","last_reissued_at":"2026-07-05T09:30:17.105647Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T09:30:17.105647Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.BM","authors_text":"Rex Ying, Tinglin Huang, Wengong Jin, Zhenqiao Song","submitted_at":"2024-06-13T20:46:51Z","abstract_excerpt":"Nucleic acid-based drugs like aptamers have recently demonstrated great therapeutic potential. However, experimental platforms for aptamer screening are costly, and the scarcity of labeled data presents a challenge for supervised methods to learn protein-aptamer binding. To this end, we develop an unsupervised learning approach based on the predicted pairwise contact map between a protein and a nucleic acid and demonstrate its effectiveness in protein-aptamer binding prediction. Our model is based on FAFormer, a novel equivariant transformer architecture that seamlessly integrates frame averag"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2406.09586","kind":"arxiv","version":3},"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/2406.09586/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":"2406.09586","created_at":"2026-07-05T09:30:17.105705+00:00"},{"alias_kind":"arxiv_version","alias_value":"2406.09586v3","created_at":"2026-07-05T09:30:17.105705+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2406.09586","created_at":"2026-07-05T09:30:17.105705+00:00"},{"alias_kind":"pith_short_12","alias_value":"TXW3QHWZYPBP","created_at":"2026-07-05T09:30:17.105705+00:00"},{"alias_kind":"pith_short_16","alias_value":"TXW3QHWZYPBPSIUG","created_at":"2026-07-05T09:30:17.105705+00:00"},{"alias_kind":"pith_short_8","alias_value":"TXW3QHWZ","created_at":"2026-07-05T09:30:17.105705+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":1,"internal_anchor_count":1,"sample":[{"citing_arxiv_id":"2507.14156","citing_title":"All-atom inverse protein folding through discrete flow matching","ref_index":18,"is_internal_anchor":true}]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC","json":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC.json","graph_json":"https://pith.science/api/pith-number/TXW3QHWZYPBPSIUGYLZLUNNXRC/graph.json","events_json":"https://pith.science/api/pith-number/TXW3QHWZYPBPSIUGYLZLUNNXRC/events.json","paper":"https://pith.science/paper/TXW3QHWZ"},"agent_actions":{"view_html":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC","download_json":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC.json","view_paper":"https://pith.science/paper/TXW3QHWZ","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2406.09586&json=true","fetch_graph":"https://pith.science/api/pith-number/TXW3QHWZYPBPSIUGYLZLUNNXRC/graph.json","fetch_events":"https://pith.science/api/pith-number/TXW3QHWZYPBPSIUGYLZLUNNXRC/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC/action/timestamp_anchor","attest_storage":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC/action/storage_attestation","attest_author":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC/action/author_attestation","sign_citation":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC/action/citation_signature","submit_replication":"https://pith.science/pith/TXW3QHWZYPBPSIUGYLZLUNNXRC/action/replication_record"}},"created_at":"2026-07-05T09:30:17.105705+00:00","updated_at":"2026-07-05T09:30:17.105705+00:00"}