{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2011:7WBYZBFNTGQ2OZAREFIW2ADMZK","short_pith_number":"pith:7WBYZBFN","canonical_record":{"source":{"id":"1104.1337","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2011-04-07T14:10:10Z","cross_cats_sorted":[],"title_canon_sha256":"cd552062470999541e0239e597fa579a231a0dc3777eb16762726c63474bd916","abstract_canon_sha256":"373dc2916025b6bf507c86d89857bc826700637d4f28c3f24ee33890ff3127e3"},"schema_version":"1.0"},"canonical_sha256":"fd838c84ad99a1a7641121516d006cca96ebeae5d08bf58dd17d71bcdd3add08","source":{"kind":"arxiv","id":"1104.1337","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1104.1337","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"arxiv_version","alias_value":"1104.1337v1","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1104.1337","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"pith_short_12","alias_value":"7WBYZBFNTGQ2","created_at":"2026-05-18T12:26:22Z"},{"alias_kind":"pith_short_16","alias_value":"7WBYZBFNTGQ2OZAR","created_at":"2026-05-18T12:26:22Z"},{"alias_kind":"pith_short_8","alias_value":"7WBYZBFN","created_at":"2026-05-18T12:26:22Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2011:7WBYZBFNTGQ2OZAREFIW2ADMZK","target":"record","payload":{"canonical_record":{"source":{"id":"1104.1337","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2011-04-07T14:10:10Z","cross_cats_sorted":[],"title_canon_sha256":"cd552062470999541e0239e597fa579a231a0dc3777eb16762726c63474bd916","abstract_canon_sha256":"373dc2916025b6bf507c86d89857bc826700637d4f28c3f24ee33890ff3127e3"},"schema_version":"1.0"},"canonical_sha256":"fd838c84ad99a1a7641121516d006cca96ebeae5d08bf58dd17d71bcdd3add08","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T00:37:05.039721Z","signature_b64":"34402wQs2AimzHfSSLDHEvGb27uiSb6iKdJIPG+xn0FyvNZq4ULMwzohON2JyRxpcb/sPm+8RJoCaYFiidm5Cw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"fd838c84ad99a1a7641121516d006cca96ebeae5d08bf58dd17d71bcdd3add08","last_reissued_at":"2026-05-18T00:37:05.039099Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T00:37:05.039099Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1104.1337","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":"2026-05-18T00:37:05Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"SizppFSCkrmoKyOREi9rOzDg9bcsSo72qkdTmeNaxY+jCtL4HKtFFH2rlOTouqSMVj5p2T0NmYsRiLk4w348CQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-24T14:49:18.141747Z"},"content_sha256":"77956a2f73a81f4ed0260f65c436f887d243713ae6f66feaebfa835d39231cad","schema_version":"1.0","event_id":"sha256:77956a2f73a81f4ed0260f65c436f887d243713ae6f66feaebfa835d39231cad"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2011:7WBYZBFNTGQ2OZAREFIW2ADMZK","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"An elastic-network based local molecular field analysis of zinc-finger proteins","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"physics.bio-ph","authors_text":"D. Asthagiri, Purushottam D. Dixit","submitted_at":"2011-04-07T14:10:10Z","abstract_excerpt":"We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue cluster by a molecular field represented by generalized harmonic restraints. The strength of the field is adjusted to reproduce the binding energy distribution of the metal with the cluster obtained in a reference all-atom simulation with empirical potentials. The quadratic field allows us to investigate analytically the protein restraints on the binding site "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1104.1337","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":""},"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":"2026-05-18T00:37:05Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"yRiP2SqPYgKgSdrhrmji9dHQ28KbQBG2Fpga7j1bQOuDA4xJfjAF7LlX+Zisx72yMLOLovsI0kCjg+Nb5BbyAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-05-24T14:49:18.142209Z"},"content_sha256":"340f2703317954d98a8f6bded60ec783691e4f529502cd1cd018c9e1b4b0f67a","schema_version":"1.0","event_id":"sha256:340f2703317954d98a8f6bded60ec783691e4f529502cd1cd018c9e1b4b0f67a"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/bundle.json","state_url":"https://pith.science/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/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":"2026-05-24T14:49:18Z","links":{"resolver":"https://pith.science/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK","bundle":"https://pith.science/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/bundle.json","state":"https://pith.science/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/state.json","well_known_bundle":"https://pith.science/.well-known/pith/7WBYZBFNTGQ2OZAREFIW2ADMZK/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2011:7WBYZBFNTGQ2OZAREFIW2ADMZK","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":"373dc2916025b6bf507c86d89857bc826700637d4f28c3f24ee33890ff3127e3","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2011-04-07T14:10:10Z","title_canon_sha256":"cd552062470999541e0239e597fa579a231a0dc3777eb16762726c63474bd916"},"schema_version":"1.0","source":{"id":"1104.1337","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1104.1337","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"arxiv_version","alias_value":"1104.1337v1","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1104.1337","created_at":"2026-05-18T00:37:05Z"},{"alias_kind":"pith_short_12","alias_value":"7WBYZBFNTGQ2","created_at":"2026-05-18T12:26:22Z"},{"alias_kind":"pith_short_16","alias_value":"7WBYZBFNTGQ2OZAR","created_at":"2026-05-18T12:26:22Z"},{"alias_kind":"pith_short_8","alias_value":"7WBYZBFN","created_at":"2026-05-18T12:26:22Z"}],"graph_snapshots":[{"event_id":"sha256:340f2703317954d98a8f6bded60ec783691e4f529502cd1cd018c9e1b4b0f67a","target":"graph","created_at":"2026-05-18T00:37:05Z","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":"We study two designed and one natural zinc-finger peptide each with the Cys2His2 (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue cluster by a molecular field represented by generalized harmonic restraints. The strength of the field is adjusted to reproduce the binding energy distribution of the metal with the cluster obtained in a reference all-atom simulation with empirical potentials. The quadratic field allows us to investigate analytically the protein restraints on the binding site ","authors_text":"D. Asthagiri, Purushottam D. Dixit","cross_cats":[],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2011-04-07T14:10:10Z","title":"An elastic-network based local molecular field analysis of zinc-finger proteins"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1104.1337","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":"sha256:77956a2f73a81f4ed0260f65c436f887d243713ae6f66feaebfa835d39231cad","target":"record","created_at":"2026-05-18T00:37:05Z","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":"373dc2916025b6bf507c86d89857bc826700637d4f28c3f24ee33890ff3127e3","cross_cats_sorted":[],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2011-04-07T14:10:10Z","title_canon_sha256":"cd552062470999541e0239e597fa579a231a0dc3777eb16762726c63474bd916"},"schema_version":"1.0","source":{"id":"1104.1337","kind":"arxiv","version":1}},"canonical_sha256":"fd838c84ad99a1a7641121516d006cca96ebeae5d08bf58dd17d71bcdd3add08","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"fd838c84ad99a1a7641121516d006cca96ebeae5d08bf58dd17d71bcdd3add08","first_computed_at":"2026-05-18T00:37:05.039099Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T00:37:05.039099Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"34402wQs2AimzHfSSLDHEvGb27uiSb6iKdJIPG+xn0FyvNZq4ULMwzohON2JyRxpcb/sPm+8RJoCaYFiidm5Cw==","signature_status":"signed_v1","signed_at":"2026-05-18T00:37:05.039721Z","signed_message":"canonical_sha256_bytes"},"source_id":"1104.1337","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:77956a2f73a81f4ed0260f65c436f887d243713ae6f66feaebfa835d39231cad","sha256:340f2703317954d98a8f6bded60ec783691e4f529502cd1cd018c9e1b4b0f67a"],"state_sha256":"5e7aedc5d84e4bb781d2390919e574e9d8a5a5f51c41e9d4784f145ca40a2de9"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Pz1ppbZ2GEI4gemIXZaFE2YgRtT9kdmFl7q+fRt/HUeCMuhKcs8ZM8LjUyoSjaq6kd8oJdgOQU52U3ahMBRxCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-05-24T14:49:18.145612Z","bundle_sha256":"8c9e80a76304fd2377b3c1d69cc7d85f6d7ac51920480814f8ffbe7aab85f569"}}