{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2023:B6RD3BHHWJBPIL6TQL6RWSWSRM","short_pith_number":"pith:B6RD3BHH","schema_version":"1.0","canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","source":{"kind":"arxiv","id":"2312.00080","version":1},"attestation_state":"computed","paper":{"title":"PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.QM","authors_text":"Bozitao Zhong, Chuanrui Wang, Jian Tang, Narendra Chaudhary, Sanchit Misra, Zuobai Zhang","submitted_at":"2023-11-30T02:37:55Z","abstract_excerpt":"Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be overly time-consuming for the development of new algorithms, and the $\\textit{in silico}$ validation with recovery and perplexity metrics is efficient but may not precisely reflect true foldability. To address this gap, we introduce two novel metrics: refoldability-based metric, which leverages high-accuracy protein structure prediction models as a proxy for w"},"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":"2312.00080","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2023-11-30T02:37:55Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"3391f88dccf72af1eb0ee7b53df9db5ad6949388a1d74c15a19f0c8e299a899d","abstract_canon_sha256":"386f6d7f50efe0b5a3e30355f317c2d397779e44375b81cdb02bafb80f9ba029"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T07:19:03.429918Z","signature_b64":"yPSvrFwlh1/Zq+1sELzMlCZWJW3nIkMdXYBM4lU7lObkWZhmgqt3gF2KC48SQpuJzgABSZVqWLhrx5InjbDvDA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","last_reissued_at":"2026-07-05T07:19:03.429427Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T07:19:03.429427Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.QM","authors_text":"Bozitao Zhong, Chuanrui Wang, Jian Tang, Narendra Chaudhary, Sanchit Misra, Zuobai Zhang","submitted_at":"2023-11-30T02:37:55Z","abstract_excerpt":"Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be overly time-consuming for the development of new algorithms, and the $\\textit{in silico}$ validation with recovery and perplexity metrics is efficient but may not precisely reflect true foldability. To address this gap, we introduce two novel metrics: refoldability-based metric, which leverages high-accuracy protein structure prediction models as a proxy for w"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2312.00080","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/2312.00080/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":"2312.00080","created_at":"2026-07-05T07:19:03.429491+00:00"},{"alias_kind":"arxiv_version","alias_value":"2312.00080v1","created_at":"2026-07-05T07:19:03.429491+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2312.00080","created_at":"2026-07-05T07:19:03.429491+00:00"},{"alias_kind":"pith_short_12","alias_value":"B6RD3BHHWJBP","created_at":"2026-07-05T07:19:03.429491+00:00"},{"alias_kind":"pith_short_16","alias_value":"B6RD3BHHWJBPIL6T","created_at":"2026-07-05T07:19:03.429491+00:00"},{"alias_kind":"pith_short_8","alias_value":"B6RD3BHH","created_at":"2026-07-05T07:19:03.429491+00:00"}],"events":[],"event_summary":{},"paper_claims":[],"inbound_citations":{"count":3,"internal_anchor_count":0,"sample":[{"citing_arxiv_id":"2606.07567","citing_title":"SurfDesign: Effective Protein Design on Molecular Surfaces","ref_index":76,"is_internal_anchor":false},{"citing_arxiv_id":"2605.10978","citing_title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","ref_index":83,"is_internal_anchor":false},{"citing_arxiv_id":"2605.10978","citing_title":"VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design","ref_index":83,"is_internal_anchor":false}]},"formal_canon":{"evidence_count":0,"sample":[],"anchors":[]},"links":{"html":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM","json":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM.json","graph_json":"https://pith.science/api/pith-number/B6RD3BHHWJBPIL6TQL6RWSWSRM/graph.json","events_json":"https://pith.science/api/pith-number/B6RD3BHHWJBPIL6TQL6RWSWSRM/events.json","paper":"https://pith.science/paper/B6RD3BHH"},"agent_actions":{"view_html":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM","download_json":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM.json","view_paper":"https://pith.science/paper/B6RD3BHH","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=2312.00080&json=true","fetch_graph":"https://pith.science/api/pith-number/B6RD3BHHWJBPIL6TQL6RWSWSRM/graph.json","fetch_events":"https://pith.science/api/pith-number/B6RD3BHHWJBPIL6TQL6RWSWSRM/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/action/timestamp_anchor","attest_storage":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/action/storage_attestation","attest_author":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/action/author_attestation","sign_citation":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/action/citation_signature","submit_replication":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/action/replication_record"}},"created_at":"2026-07-05T07:19:03.429491+00:00","updated_at":"2026-07-05T07:19:03.429491+00:00"}