{"record_type":"pith_number_record","schema_url":"https://pith.science/schemas/pith-number/v1.json","pith_number":"pith:2013:H7QNU3GOZ4SVFZHXGFUX6TFVTK","short_pith_number":"pith:H7QNU3GO","schema_version":"1.0","canonical_sha256":"3fe0da6ccecf2552e4f731697f4cb59aa6862c41270b8a0f64d2e000c4b1714f","source":{"kind":"arxiv","id":"1308.4342","version":2},"attestation_state":"computed","paper":{"title":"A new formulation of protein evolutionary models that account for structural constraints","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"q-bio.PE","authors_text":"Andrew J. Bordner, Hans D. Mittelmann","submitted_at":"2013-08-20T16:11:26Z","abstract_excerpt":"Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid sites. This is mainly due to the difficulty in formulating a computationally tractable model since rate matrices can no longer be used. Here we introduce a general framework, based on factor graphs, for constructing probabilistic models of protein evolution with site interdependence. Conveniently, efficient approximate inference algorithms, like Belief Propaga"},"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":"1308.4342","kind":"arxiv","version":2},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"q-bio.PE","submitted_at":"2013-08-20T16:11:26Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"163004a98a4a07fb4b0ecd108fda600bd3ee1678b2cc7dacbcf5a3983af13be2","abstract_canon_sha256":"a23bd7beedd20aa2b994826dc4077b5cd9219e6a54e292f7348b0f421959bb0e"},"schema_version":"1.0"},"receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:05:37.664968Z","signature_b64":"oQ18NYbPtylodcSrENE0sqW/5yimvaDH03NPEjXJeCFm9jNBvUC+Ny+bct7dQ5izJMZ/YTkYVxJCcLP4zPjKCA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"3fe0da6ccecf2552e4f731697f4cb59aa6862c41270b8a0f64d2e000c4b1714f","last_reissued_at":"2026-05-18T03:05:37.664435Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:05:37.664435Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"graph_snapshot":{"paper":{"title":"A new formulation of protein evolutionary models that account for structural constraints","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"q-bio.PE","authors_text":"Andrew J. Bordner, Hans D. Mittelmann","submitted_at":"2013-08-20T16:11:26Z","abstract_excerpt":"Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid sites. This is mainly due to the difficulty in formulating a computationally tractable model since rate matrices can no longer be used. Here we introduce a general framework, based on factor graphs, for constructing probabilistic models of protein evolution with site interdependence. Conveniently, efficient approximate inference algorithms, like Belief Propaga"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1308.4342","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"},"aliases":[{"alias_kind":"arxiv","alias_value":"1308.4342","created_at":"2026-05-18T03:05:37.664512+00:00"},{"alias_kind":"arxiv_version","alias_value":"1308.4342v2","created_at":"2026-05-18T03:05:37.664512+00:00"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1308.4342","created_at":"2026-05-18T03:05:37.664512+00:00"},{"alias_kind":"pith_short_12","alias_value":"H7QNU3GOZ4SV","created_at":"2026-05-18T12:27:46.883200+00:00"},{"alias_kind":"pith_short_16","alias_value":"H7QNU3GOZ4SVFZHX","created_at":"2026-05-18T12:27:46.883200+00:00"},{"alias_kind":"pith_short_8","alias_value":"H7QNU3GO","created_at":"2026-05-18T12:27:46.883200+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/H7QNU3GOZ4SVFZHXGFUX6TFVTK","json":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK.json","graph_json":"https://pith.science/api/pith-number/H7QNU3GOZ4SVFZHXGFUX6TFVTK/graph.json","events_json":"https://pith.science/api/pith-number/H7QNU3GOZ4SVFZHXGFUX6TFVTK/events.json","paper":"https://pith.science/paper/H7QNU3GO"},"agent_actions":{"view_html":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK","download_json":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK.json","view_paper":"https://pith.science/paper/H7QNU3GO","resolve_alias":"https://pith.science/api/pith-number/resolve?arxiv=1308.4342&json=true","fetch_graph":"https://pith.science/api/pith-number/H7QNU3GOZ4SVFZHXGFUX6TFVTK/graph.json","fetch_events":"https://pith.science/api/pith-number/H7QNU3GOZ4SVFZHXGFUX6TFVTK/events.json","actions":{"anchor_timestamp":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK/action/timestamp_anchor","attest_storage":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK/action/storage_attestation","attest_author":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK/action/author_attestation","sign_citation":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK/action/citation_signature","submit_replication":"https://pith.science/pith/H7QNU3GOZ4SVFZHXGFUX6TFVTK/action/replication_record"}},"created_at":"2026-05-18T03:05:37.664512+00:00","updated_at":"2026-05-18T03:05:37.664512+00:00"}