{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2023:B6RD3BHHWJBPIL6TQL6RWSWSRM","short_pith_number":"pith:B6RD3BHH","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"},"canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","source":{"kind":"arxiv","id":"2312.00080","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2312.00080","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"arxiv_version","alias_value":"2312.00080v1","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2312.00080","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_12","alias_value":"B6RD3BHHWJBP","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_16","alias_value":"B6RD3BHHWJBPIL6T","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_8","alias_value":"B6RD3BHH","created_at":"2026-07-05T07:19:03Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2023:B6RD3BHHWJBPIL6TQL6RWSWSRM","target":"record","payload":{"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"},"canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","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"},"source_kind":"arxiv","source_id":"2312.00080","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":"2026-07-05T07:19:03Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"JntwAAQXWyF3KwpdPerd0vtmVmyMOzTa8DJQqTvN5Tv2FgolUBXq/R85zogfRzqJv20I4OpdvhFM6qi0tBWVDA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-15T08:06:19.091755Z"},"content_sha256":"dcfb18b1deb42c6c23e427cbbabe1731ee01c15cbc3fa737c0d44fd7c92eff7d","schema_version":"1.0","event_id":"sha256:dcfb18b1deb42c6c23e427cbbabe1731ee01c15cbc3fa737c0d44fd7c92eff7d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2023:B6RD3BHHWJBPIL6TQL6RWSWSRM","target":"graph","payload":{"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"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-07-05T07:19:03Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"/bOT1WMHzkA8AD9+Z2u52wVmgfyGHupD4u8bkcuSesZP71uuSTeC86R036P97CxpddSbbjAcaHfmEbRRC547CA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-15T08:06:19.092781Z"},"content_sha256":"3f8e17a66122c43ec46a588d89f2caeefaee893c813d6a9877833c4d801f115c","schema_version":"1.0","event_id":"sha256:3f8e17a66122c43ec46a588d89f2caeefaee893c813d6a9877833c4d801f115c"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/bundle.json","state_url":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/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":"2026-08-15T08:06:19Z","links":{"resolver":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM","bundle":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/bundle.json","state":"https://pith.science/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/state.json","well_known_bundle":"https://pith.science/.well-known/pith/B6RD3BHHWJBPIL6TQL6RWSWSRM/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2023:B6RD3BHHWJBPIL6TQL6RWSWSRM","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":"386f6d7f50efe0b5a3e30355f317c2d397779e44375b81cdb02bafb80f9ba029","cross_cats_sorted":["cs.LG"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2023-11-30T02:37:55Z","title_canon_sha256":"3391f88dccf72af1eb0ee7b53df9db5ad6949388a1d74c15a19f0c8e299a899d"},"schema_version":"1.0","source":{"id":"2312.00080","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2312.00080","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"arxiv_version","alias_value":"2312.00080v1","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2312.00080","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_12","alias_value":"B6RD3BHHWJBP","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_16","alias_value":"B6RD3BHHWJBPIL6T","created_at":"2026-07-05T07:19:03Z"},{"alias_kind":"pith_short_8","alias_value":"B6RD3BHH","created_at":"2026-07-05T07:19:03Z"}],"graph_snapshots":[{"event_id":"sha256:3f8e17a66122c43ec46a588d89f2caeefaee893c813d6a9877833c4d801f115c","target":"graph","created_at":"2026-07-05T07:19:03Z","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/2312.00080/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"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","authors_text":"Bozitao Zhong, Chuanrui Wang, Jian Tang, Narendra Chaudhary, Sanchit Misra, Zuobai Zhang","cross_cats":["cs.LG"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2023-11-30T02:37:55Z","title":"PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2312.00080","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:dcfb18b1deb42c6c23e427cbbabe1731ee01c15cbc3fa737c0d44fd7c92eff7d","target":"record","created_at":"2026-07-05T07:19:03Z","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":"386f6d7f50efe0b5a3e30355f317c2d397779e44375b81cdb02bafb80f9ba029","cross_cats_sorted":["cs.LG"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.QM","submitted_at":"2023-11-30T02:37:55Z","title_canon_sha256":"3391f88dccf72af1eb0ee7b53df9db5ad6949388a1d74c15a19f0c8e299a899d"},"schema_version":"1.0","source":{"id":"2312.00080","kind":"arxiv","version":1}},"canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"0fa23d84e7b242f42fd382fd1b4ad28b339ace1d2a98b2831d03fe52fe0cbbf2","first_computed_at":"2026-07-05T07:19:03.429427Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T07:19:03.429427Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"yPSvrFwlh1/Zq+1sELzMlCZWJW3nIkMdXYBM4lU7lObkWZhmgqt3gF2KC48SQpuJzgABSZVqWLhrx5InjbDvDA==","signature_status":"signed_v1","signed_at":"2026-07-05T07:19:03.429918Z","signed_message":"canonical_sha256_bytes"},"source_id":"2312.00080","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:dcfb18b1deb42c6c23e427cbbabe1731ee01c15cbc3fa737c0d44fd7c92eff7d","sha256:3f8e17a66122c43ec46a588d89f2caeefaee893c813d6a9877833c4d801f115c"],"state_sha256":"67baa4d3e1f9400a19f704617f095966c8b79b493e62fe5ce0b009af1bfe25a1"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"CTdjT65jk9y4cttatzMUiBaJyzfcahTpKUbBxlUoM4sj1rlEcF30smVMHqsjx7cMbVIslSf0c3O49wkXph6+BQ==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-15T08:06:19.096805Z","bundle_sha256":"fac659de0d09b8facf9f2840eda2d059bbfde7b390f48a044d232445b4d03c2d"}}