{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2026:3ZN46OBQW23QDMOPNKY6FJ7KW4","short_pith_number":"pith:3ZN46OBQ","schema_version":"1.0","canonical_sha256":"de5bcf3830b6b701b1cf6ab1e2a7eab72de2346c68eb51aa1ff72d318d37fa28","source":{"kind":"arxiv","id":"2605.27413","version":1},"attestation_state":"computed","paper":{"title":"Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Chen Wei, Fanding Xu, Lin Wang, Minghao Sun, Tianrui Jia, Yang Zhang, Yihang Zhou, Zhiyuan Liu","submitted_at":"2026-05-15T04:45:47Z","abstract_excerpt":"Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit ligand constraints. Although continuous diffusion and flow-based models support ligand-aware design in coordinate or latent spaces, existing discrete diffusion protein language models mainly operate over sequence or structure tokens without direct small-molecule conditioning. We introduce \\textbf{ProtLiD$^2$}, a \\textbf{Prot}ein \\textbf{L}igand-conditioned \\textb"},"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":"2605.27413","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2026-05-15T04:45:47Z","cross_cats_sorted":["cs.AI"],"title_canon_sha256":"82e31a1a457a109407aded989eb0ef7e75e365ef07acaccca49656ba626dcebe","abstract_canon_sha256":"ed1cf422a661d928db7e15c895e9b15cc0dfb90d52acd5181b81714592f91fdf"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-28T00:05:17.575113Z","signature_b64":"+VKn0UOjxe5nzTQ+0e30VA1cmR3XQ8yfqc1w50RfNqim0iQ5XuoS7J1OMJ9wGAn+VpdHg4n76GWsX2u8lJrhDw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"de5bcf3830b6b701b1cf6ab1e2a7eab72de2346c68eb51aa1ff72d318d37fa28","last_reissued_at":"2026-05-28T00:05:17.574369Z","signature_status":"signed_v1","first_computed_at":"2026-05-28T00:05:17.574369Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.BM","authors_text":"Chen Wei, Fanding Xu, Lin Wang, Minghao Sun, Tianrui Jia, Yang Zhang, Yihang Zhou, Zhiyuan Liu","submitted_at":"2026-05-15T04:45:47Z","abstract_excerpt":"Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit ligand constraints. Although continuous diffusion and flow-based models support ligand-aware design in coordinate or latent spaces, existing discrete diffusion protein language models mainly operate over sequence or structure tokens without direct small-molecule conditioning. We introduce \\textbf{ProtLiD$^2$}, a \\textbf{Prot}ein \\textbf{L}igand-conditioned \\textb"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.27413","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/2605.27413/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":"2605.27413","created_at":"2026-05-28T00:05:17.574483+00:00"},{"alias_kind":"arxiv_version","alias_value":"2605.27413v1","created_at":"2026-05-28T00:05:17.574483+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2605.27413","created_at":"2026-05-28T00:05:17.574483+00:00"},{"alias_kind":"pith_short_12","alias_value":"3ZN46OBQW23Q","created_at":"2026-05-28T00:05:17.574483+00:00"},{"alias_kind":"pith_short_16","alias_value":"3ZN46OBQW23QDMOP","created_at":"2026-05-28T00:05:17.574483+00:00"},{"alias_kind":"pith_short_8","alias_value":"3ZN46OBQ","created_at":"2026-05-28T00:05:17.574483+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/3ZN46OBQW23QDMOPNKY6FJ7KW4","json":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4.json","graph_json":"https://pith.science/api/pith-number/3ZN46OBQW23QDMOPNKY6FJ7KW4/graph.json","events_json":"https://pith.science/api/pith-number/3ZN46OBQW23QDMOPNKY6FJ7KW4/events.json","paper":"https://pith.science/paper/3ZN46OBQ"},"agent_actions":{"view_html":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4","download_json":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4.json","view_paper":"https://pith.science/paper/3ZN46OBQ","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2605.27413&json=true","fetch_graph":"https://pith.science/api/pith-number/3ZN46OBQW23QDMOPNKY6FJ7KW4/graph.json","fetch_events":"https://pith.science/api/pith-number/3ZN46OBQW23QDMOPNKY6FJ7KW4/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4/action/timestamp_anchor","attest_storage":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4/action/storage_attestation","attest_author":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4/action/author_attestation","sign_citation":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4/action/citation_signature","submit_replication":"https://pith.science/pith/3ZN46OBQW23QDMOPNKY6FJ7KW4/action/replication_record"}},"created_at":"2026-05-28T00:05:17.574483+00:00","updated_at":"2026-05-28T00:05:17.574483+00:00"}