{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2017:Y3KMX2LQV46U4UJI6MRC7TL45S","short_pith_number":"pith:Y3KMX2LQ","canonical_record":{"source":{"id":"1706.01345","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2017-06-05T14:24:42Z","cross_cats_sorted":["physics.bio-ph"],"title_canon_sha256":"e242d6e995a88e750b80ebd1e8d522db81a1bd71a3b2f666def3df1cd06e3961","abstract_canon_sha256":"f77cb23c3dab183f2d5c1bafee83b37722a843084f304c57b63ebe1836e7bc9d"},"schema_version":"1.0"},"canonical_sha256":"c6d4cbe970af3d4e5128f3222fcd7cec846c3453d1a1050f6ad58d4e4ce5f3ab","source":{"kind":"arxiv","id":"1706.01345","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1706.01345","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"arxiv_version","alias_value":"1706.01345v2","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1706.01345","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"pith_short_12","alias_value":"Y3KMX2LQV46U","created_at":"2026-05-18T12:31:56Z"},{"alias_kind":"pith_short_16","alias_value":"Y3KMX2LQV46U4UJI","created_at":"2026-05-18T12:31:56Z"},{"alias_kind":"pith_short_8","alias_value":"Y3KMX2LQ","created_at":"2026-05-18T12:31:56Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2017:Y3KMX2LQV46U4UJI6MRC7TL45S","target":"record","payload":{"canonical_record":{"source":{"id":"1706.01345","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2017-06-05T14:24:42Z","cross_cats_sorted":["physics.bio-ph"],"title_canon_sha256":"e242d6e995a88e750b80ebd1e8d522db81a1bd71a3b2f666def3df1cd06e3961","abstract_canon_sha256":"f77cb23c3dab183f2d5c1bafee83b37722a843084f304c57b63ebe1836e7bc9d"},"schema_version":"1.0"},"canonical_sha256":"c6d4cbe970af3d4e5128f3222fcd7cec846c3453d1a1050f6ad58d4e4ce5f3ab","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:42:57.005768Z","signature_b64":"g9cKEMAshoFysH1wtra6iwpvZ0p6yeJZiDnOOWnXU/6wAkeQb2R1fhrtP5T3AtIJxo9oT0bPfLXo9eKIym8pCw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"c6d4cbe970af3d4e5128f3222fcd7cec846c3453d1a1050f6ad58d4e4ce5f3ab","last_reissued_at":"2026-05-18T00:42:57.004952Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:42:57.004952Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1706.01345","source_version":2,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-05-18T00:42:57Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"mNId8YHHt18GzNGHwHyNxhBMxQIZqrE5eZvp1z1NGZlRxdjAU4EZI4E/GxL6K+z0RapZXEmMnxO4g2rdsxUCCg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T14:08:30.363389Z"},"content_sha256":"d90f7bf800bc06548aa61948da1e7c751905f18e94819ba860f424530077101d","schema_version":"1.0","event_id":"sha256:d90f7bf800bc06548aa61948da1e7c751905f18e94819ba860f424530077101d"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2017:Y3KMX2LQV46U4UJI6MRC7TL45S","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Virtual reality analysis of intrinsic protein geometry with applications to cis peptide planes","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["physics.bio-ph"],"primary_cat":"q-bio.BM","authors_text":"Antti J. Niemi, Jianfeng He, Jin Dai, Nevena Ilieva, Xubiao Peng, Yanzhen Hou","submitted_at":"2017-06-05T14:24:42Z","abstract_excerpt":"A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we in"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1706.01345","kind":"arxiv","version":2},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"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":"2026-05-18T00:42:57Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"B+y4IMSWwIeUNbV4ZKaSfMYxMI66lL6gDpZQ5N1jz8bVmemqPoZ2+FYkxUMx0ik8QQejVcwrrjyGrLwi5qb7AA==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-27T14:08:30.363848Z"},"content_sha256":"b96eaaab5090b44218f32156568b4a7ba7c86f90708dd045110b2c283a345e3f","schema_version":"1.0","event_id":"sha256:b96eaaab5090b44218f32156568b4a7ba7c86f90708dd045110b2c283a345e3f"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/bundle.json","state_url":"https://pith.science/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/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":"2026-05-27T14:08:30Z","links":{"resolver":"https://pith.science/pith/Y3KMX2LQV46U4UJI6MRC7TL45S","bundle":"https://pith.science/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/bundle.json","state":"https://pith.science/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/state.json","well_known_bundle":"https://pith.science/.well-known/pith/Y3KMX2LQV46U4UJI6MRC7TL45S/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2017:Y3KMX2LQV46U4UJI6MRC7TL45S","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":"f77cb23c3dab183f2d5c1bafee83b37722a843084f304c57b63ebe1836e7bc9d","cross_cats_sorted":["physics.bio-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2017-06-05T14:24:42Z","title_canon_sha256":"e242d6e995a88e750b80ebd1e8d522db81a1bd71a3b2f666def3df1cd06e3961"},"schema_version":"1.0","source":{"id":"1706.01345","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1706.01345","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"arxiv_version","alias_value":"1706.01345v2","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1706.01345","created_at":"2026-05-18T00:42:57Z"},{"alias_kind":"pith_short_12","alias_value":"Y3KMX2LQV46U","created_at":"2026-05-18T12:31:56Z"},{"alias_kind":"pith_short_16","alias_value":"Y3KMX2LQV46U4UJI","created_at":"2026-05-18T12:31:56Z"},{"alias_kind":"pith_short_8","alias_value":"Y3KMX2LQ","created_at":"2026-05-18T12:31:56Z"}],"graph_snapshots":[{"event_id":"sha256:b96eaaab5090b44218f32156568b4a7ba7c86f90708dd045110b2c283a345e3f","target":"graph","created_at":"2026-05-18T00:42:57Z","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"},"paper":{"abstract_excerpt":"A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic geometric structures, due to the peptide planes and the side chains. Here we adapt and develop modern 3D virtual reality techniques to scrutinize the atomic geometry along a protein backbone, in the vicinity of a peptide plane. For this we compare backbone geometry-based (extrinsic) and structure-based (intrinsic) coordinate systems, and as an example we in","authors_text":"Antti J. Niemi, Jianfeng He, Jin Dai, Nevena Ilieva, Xubiao Peng, Yanzhen Hou","cross_cats":["physics.bio-ph"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2017-06-05T14:24:42Z","title":"Virtual reality analysis of intrinsic protein geometry with applications to cis peptide planes"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1706.01345","kind":"arxiv","version":2},"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:d90f7bf800bc06548aa61948da1e7c751905f18e94819ba860f424530077101d","target":"record","created_at":"2026-05-18T00:42:57Z","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":"f77cb23c3dab183f2d5c1bafee83b37722a843084f304c57b63ebe1836e7bc9d","cross_cats_sorted":["physics.bio-ph"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.BM","submitted_at":"2017-06-05T14:24:42Z","title_canon_sha256":"e242d6e995a88e750b80ebd1e8d522db81a1bd71a3b2f666def3df1cd06e3961"},"schema_version":"1.0","source":{"id":"1706.01345","kind":"arxiv","version":2}},"canonical_sha256":"c6d4cbe970af3d4e5128f3222fcd7cec846c3453d1a1050f6ad58d4e4ce5f3ab","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"c6d4cbe970af3d4e5128f3222fcd7cec846c3453d1a1050f6ad58d4e4ce5f3ab","first_computed_at":"2026-05-18T00:42:57.004952Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:42:57.004952Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"g9cKEMAshoFysH1wtra6iwpvZ0p6yeJZiDnOOWnXU/6wAkeQb2R1fhrtP5T3AtIJxo9oT0bPfLXo9eKIym8pCw==","signature_status":"signed_v1","signed_at":"2026-05-18T00:42:57.005768Z","signed_message":"canonical_sha256_bytes"},"source_id":"1706.01345","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:d90f7bf800bc06548aa61948da1e7c751905f18e94819ba860f424530077101d","sha256:b96eaaab5090b44218f32156568b4a7ba7c86f90708dd045110b2c283a345e3f"],"state_sha256":"49f401e9d6bbb9b9be6e090c433f6bc2063f6bee87c3cc256a22810c678f9579"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"IpAk5V/cES1YYdimkC2MCZzCaaaJXpYXxbtiGM0CpdDDtJTMX4Iqg7luGHB+QuPQ1qr3QawbDxE1Or+aEspTBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-27T14:08:30.367240Z","bundle_sha256":"1e1186b84804ff6cbed8409369ca5fa019f03f65295f6365d843771fa76b3dc7"}}