{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2013:53I5NLRGYBDA4ML3UGLIHA3UAA","short_pith_number":"pith:53I5NLRG","canonical_record":{"source":{"id":"1308.2388","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-08-11T12:45:14Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"ec5035a4f93200440ed585411d7735efed570e8cada45d80823bc70be84f6069","abstract_canon_sha256":"4aaea9736c35e0f66ab4f23bb443a2329881112af1c183986ff3a356ce37b320"},"schema_version":"1.0"},"canonical_sha256":"eed1d6ae26c0460e317ba19683837400207970978303646b20c8e3e7a5e1256d","source":{"kind":"arxiv","id":"1308.2388","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1308.2388","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"arxiv_version","alias_value":"1308.2388v1","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1308.2388","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"pith_short_12","alias_value":"53I5NLRGYBDA","created_at":"2026-05-18T12:27:34Z"},{"alias_kind":"pith_short_16","alias_value":"53I5NLRGYBDA4ML3","created_at":"2026-05-18T12:27:34Z"},{"alias_kind":"pith_short_8","alias_value":"53I5NLRG","created_at":"2026-05-18T12:27:34Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2013:53I5NLRGYBDA4ML3UGLIHA3UAA","target":"record","payload":{"canonical_record":{"source":{"id":"1308.2388","kind":"arxiv","version":1},"metadata":{"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-08-11T12:45:14Z","cross_cats_sorted":["q-bio.BM"],"title_canon_sha256":"ec5035a4f93200440ed585411d7735efed570e8cada45d80823bc70be84f6069","abstract_canon_sha256":"4aaea9736c35e0f66ab4f23bb443a2329881112af1c183986ff3a356ce37b320"},"schema_version":"1.0"},"canonical_sha256":"eed1d6ae26c0460e317ba19683837400207970978303646b20c8e3e7a5e1256d","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-05-18T03:16:07.583500Z","signature_b64":"Be0237EDmIBN+loctorRkVeKsvURlk5PXfp+hgUQ2HHhnl0GvST+K9DH6JKAMbUhU5h7ZdoIgnM6nuh/hKhdCw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"eed1d6ae26c0460e317ba19683837400207970978303646b20c8e3e7a5e1256d","last_reissued_at":"2026-05-18T03:16:07.582812Z","signature_status":"signed_v1","first_computed_at":"2026-05-18T03:16:07.582812Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"1308.2388","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":"2026-05-18T03:16:07Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"Ysg96m3w/tAyUHIgbreIpxJxyesi0weY9c5Z7QVzRntZ6W6+ZjBJffvTS9egtqaZNOoZ/3FD89AkFxbizEIfDw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-05T01:37:33.912016Z"},"content_sha256":"8c0e9a40321d95df68a31e67459169ed18661a2b716ce8910d2e28f326511490","schema_version":"1.0","event_id":"sha256:8c0e9a40321d95df68a31e67459169ed18661a2b716ce8910d2e28f326511490"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2013:53I5NLRGYBDA4ML3UGLIHA3UAA","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.BM"],"primary_cat":"physics.bio-ph","authors_text":"Andrzej Kolinski, Dominik Gront, Jacek Wabik, Maksim Kouza, Sebastian Kmiecik","submitted_at":"2013-08-11T12:45:14Z","abstract_excerpt":"We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting fr"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1308.2388","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":"2026-05-18T03:16:07Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"W/dsCAP6GXnLYpmlINSdupNCuAlsIo/joN1iv8w+nuqqlnL+D5h4JTOMXsMl+5ReN6dptOKsVYMYkBmLwsCECw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-06-05T01:37:33.912501Z"},"content_sha256":"c8b2737adcbcb95d8fb9298caf9843c9b2568d8e11f09dfadbd785ae77c29d38","schema_version":"1.0","event_id":"sha256:c8b2737adcbcb95d8fb9298caf9843c9b2568d8e11f09dfadbd785ae77c29d38"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/bundle.json","state_url":"https://pith.science/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/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":"2026-06-05T01:37:33Z","links":{"resolver":"https://pith.science/pith/53I5NLRGYBDA4ML3UGLIHA3UAA","bundle":"https://pith.science/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/bundle.json","state":"https://pith.science/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/state.json","well_known_bundle":"https://pith.science/.well-known/pith/53I5NLRGYBDA4ML3UGLIHA3UAA/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2013:53I5NLRGYBDA4ML3UGLIHA3UAA","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":"4aaea9736c35e0f66ab4f23bb443a2329881112af1c183986ff3a356ce37b320","cross_cats_sorted":["q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-08-11T12:45:14Z","title_canon_sha256":"ec5035a4f93200440ed585411d7735efed570e8cada45d80823bc70be84f6069"},"schema_version":"1.0","source":{"id":"1308.2388","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"1308.2388","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"arxiv_version","alias_value":"1308.2388v1","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.1308.2388","created_at":"2026-05-18T03:16:07Z"},{"alias_kind":"pith_short_12","alias_value":"53I5NLRGYBDA","created_at":"2026-05-18T12:27:34Z"},{"alias_kind":"pith_short_16","alias_value":"53I5NLRGYBDA4ML3","created_at":"2026-05-18T12:27:34Z"},{"alias_kind":"pith_short_8","alias_value":"53I5NLRG","created_at":"2026-05-18T12:27:34Z"}],"graph_snapshots":[{"event_id":"sha256:c8b2737adcbcb95d8fb9298caf9843c9b2568d8e11f09dfadbd785ae77c29d38","target":"graph","created_at":"2026-05-18T03:16:07Z","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 describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting fr","authors_text":"Andrzej Kolinski, Dominik Gront, Jacek Wabik, Maksim Kouza, Sebastian Kmiecik","cross_cats":["q-bio.BM"],"headline":"","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-08-11T12:45:14Z","title":"Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1308.2388","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":"sha256:8c0e9a40321d95df68a31e67459169ed18661a2b716ce8910d2e28f326511490","target":"record","created_at":"2026-05-18T03:16:07Z","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":"4aaea9736c35e0f66ab4f23bb443a2329881112af1c183986ff3a356ce37b320","cross_cats_sorted":["q-bio.BM"],"license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","primary_cat":"physics.bio-ph","submitted_at":"2013-08-11T12:45:14Z","title_canon_sha256":"ec5035a4f93200440ed585411d7735efed570e8cada45d80823bc70be84f6069"},"schema_version":"1.0","source":{"id":"1308.2388","kind":"arxiv","version":1}},"canonical_sha256":"eed1d6ae26c0460e317ba19683837400207970978303646b20c8e3e7a5e1256d","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"eed1d6ae26c0460e317ba19683837400207970978303646b20c8e3e7a5e1256d","first_computed_at":"2026-05-18T03:16:07.582812Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-05-18T03:16:07.582812Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"Be0237EDmIBN+loctorRkVeKsvURlk5PXfp+hgUQ2HHhnl0GvST+K9DH6JKAMbUhU5h7ZdoIgnM6nuh/hKhdCw==","signature_status":"signed_v1","signed_at":"2026-05-18T03:16:07.583500Z","signed_message":"canonical_sha256_bytes"},"source_id":"1308.2388","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:8c0e9a40321d95df68a31e67459169ed18661a2b716ce8910d2e28f326511490","sha256:c8b2737adcbcb95d8fb9298caf9843c9b2568d8e11f09dfadbd785ae77c29d38"],"state_sha256":"857df832d11ed718eb2820c278765716fb80cd60b63340c46d80a1968785e7bf"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"EUSXqeOngrVEsdM10s6ifukhyqyhymdyDlfhl4CeGlrg03c8xD9R5LJbKH5tvn/o6v0WSul0V+Q4Yuuqc3cfBA==","signed_message":"bundle_sha256_bytes","signed_at":"2026-06-05T01:37:33.915268Z","bundle_sha256":"9dd34ec078599606d1831b0d0ea9e2aef797bb723ac4da06d620530ccd5c4327"}}