{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2021:SUOS67OTVGHK7W67KHIE263WB4","short_pith_number":"pith:SUOS67OT","canonical_record":{"source":{"id":"2105.06222","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2021-05-13T12:22:49Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"6b6a16cd07c2208a264917a3751ad325240c07eedc3b85c98e3ecd80e4764063","abstract_canon_sha256":"f1cc51a3f21606f069c8a4e2d161d9d3565903d15e21549bfb5accfcca108aa0"},"schema_version":"1.0"},"canonical_sha256":"951d2f7dd3a98eafdbdf51d04d7b760f16d4ae8cfb369aa29d3bbfc7b932e696","source":{"kind":"arxiv","id":"2105.06222","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2105.06222","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"arxiv_version","alias_value":"2105.06222v2","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2105.06222","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_12","alias_value":"SUOS67OTVGHK","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_16","alias_value":"SUOS67OTVGHK7W67","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_8","alias_value":"SUOS67OT","created_at":"2026-07-05T05:55:55Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2021:SUOS67OTVGHK7W67KHIE263WB4","target":"record","payload":{"canonical_record":{"source":{"id":"2105.06222","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2021-05-13T12:22:49Z","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"title_canon_sha256":"6b6a16cd07c2208a264917a3751ad325240c07eedc3b85c98e3ecd80e4764063","abstract_canon_sha256":"f1cc51a3f21606f069c8a4e2d161d9d3565903d15e21549bfb5accfcca108aa0"},"schema_version":"1.0"},"canonical_sha256":"951d2f7dd3a98eafdbdf51d04d7b760f16d4ae8cfb369aa29d3bbfc7b932e696","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T05:55:55.855064Z","signature_b64":"LRW+BYx2xCfkoi4in2bfsxvgsAfk8SWeySxAn72im1ZEe8iD5D62yJDO97PSwLGDtB/Mmz4eosR4KS6kkXm4Cg==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"951d2f7dd3a98eafdbdf51d04d7b760f16d4ae8cfb369aa29d3bbfc7b932e696","last_reissued_at":"2026-07-05T05:55:55.854564Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T05:55:55.854564Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2105.06222","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":"2026-07-05T05:55:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"wd58v1hucZCuzVa6/joQ/L5Q1DVX/WiJPmXahphdJwsQELbDK4O3yESU/k1j79EXqDKkH8MqgC1eVFQpt3FjAQ==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T10:49:54.794812Z"},"content_sha256":"7bf5470d43334901d164923d5f8805e58ba3bb63a834f7c3420bc8bfac44cf55","schema_version":"1.0","event_id":"sha256:7bf5470d43334901d164923d5f8805e58ba3bb63a834f7c3420bc8bfac44cf55"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2021:SUOS67OTVGHK7W67KHIE263WB4","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["physics.bio-ph","physics.chem-ph"],"primary_cat":"q-bio.BM","authors_text":"Antonia S. J. S. Mey, Christina E.M. Schindler, Christopher I. Bayly, David F. Hahn, David L. Mobley, Gary Tresadern, Gregory L. Warren, Hannah E. Bruce Macdonald, John D. Chodera, Laura Perez Benito, Vytautas Gapsys","submitted_at":"2021-05-13T12:22:49Z","abstract_excerpt":"Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems (benchmarking) becomes critical to provide users with an assessment of the accuracy expected when these methods are applied within their domain of applicability, and developers with a way to assess the expected impact of new methodologies. These assessments require construction of a benchmark - a set of well-prepared, high quality systems with corresponding experimental "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2105.06222","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2105.06222/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":"2026-07-05T05:55:55Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"mViAxFwQB8x33PfieZUdVMpS+okbvcVGfaBHVrgdv8d1ypH6ExBc6sNqPzeIAQbLY8F6gKjXQ2jGDj379+eUCw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-04T10:49:54.795324Z"},"content_sha256":"662864c91e996c8d48ca89687f7b95ea3fb6341a314720bcd0a17afca8bad9fe","schema_version":"1.0","event_id":"sha256:662864c91e996c8d48ca89687f7b95ea3fb6341a314720bcd0a17afca8bad9fe"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/SUOS67OTVGHK7W67KHIE263WB4/bundle.json","state_url":"https://pith.science/pith/SUOS67OTVGHK7W67KHIE263WB4/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/SUOS67OTVGHK7W67KHIE263WB4/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":"2026-08-04T10:49:54Z","links":{"resolver":"https://pith.science/pith/SUOS67OTVGHK7W67KHIE263WB4","bundle":"https://pith.science/pith/SUOS67OTVGHK7W67KHIE263WB4/bundle.json","state":"https://pith.science/pith/SUOS67OTVGHK7W67KHIE263WB4/state.json","well_known_bundle":"https://pith.science/.well-known/pith/SUOS67OTVGHK7W67KHIE263WB4/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2021:SUOS67OTVGHK7W67KHIE263WB4","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":"f1cc51a3f21606f069c8a4e2d161d9d3565903d15e21549bfb5accfcca108aa0","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2021-05-13T12:22:49Z","title_canon_sha256":"6b6a16cd07c2208a264917a3751ad325240c07eedc3b85c98e3ecd80e4764063"},"schema_version":"1.0","source":{"id":"2105.06222","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2105.06222","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"arxiv_version","alias_value":"2105.06222v2","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2105.06222","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_12","alias_value":"SUOS67OTVGHK","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_16","alias_value":"SUOS67OTVGHK7W67","created_at":"2026-07-05T05:55:55Z"},{"alias_kind":"pith_short_8","alias_value":"SUOS67OT","created_at":"2026-07-05T05:55:55Z"}],"graph_snapshots":[{"event_id":"sha256:662864c91e996c8d48ca89687f7b95ea3fb6341a314720bcd0a17afca8bad9fe","target":"graph","created_at":"2026-07-05T05:55:55Z","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/2105.06222/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems (benchmarking) becomes critical to provide users with an assessment of the accuracy expected when these methods are applied within their domain of applicability, and developers with a way to assess the expected impact of new methodologies. These assessments require construction of a benchmark - a set of well-prepared, high quality systems with corresponding experimental ","authors_text":"Antonia S. J. S. Mey, Christina E.M. Schindler, Christopher I. Bayly, David F. Hahn, David L. Mobley, Gary Tresadern, Gregory L. Warren, Hannah E. Bruce Macdonald, John D. Chodera, Laura Perez Benito, Vytautas Gapsys","cross_cats":["physics.bio-ph","physics.chem-ph"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2021-05-13T12:22:49Z","title":"Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2105.06222","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":"sha256:7bf5470d43334901d164923d5f8805e58ba3bb63a834f7c3420bc8bfac44cf55","target":"record","created_at":"2026-07-05T05:55:55Z","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":"f1cc51a3f21606f069c8a4e2d161d9d3565903d15e21549bfb5accfcca108aa0","cross_cats_sorted":["physics.bio-ph","physics.chem-ph"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2021-05-13T12:22:49Z","title_canon_sha256":"6b6a16cd07c2208a264917a3751ad325240c07eedc3b85c98e3ecd80e4764063"},"schema_version":"1.0","source":{"id":"2105.06222","kind":"arxiv","version":2}},"canonical_sha256":"951d2f7dd3a98eafdbdf51d04d7b760f16d4ae8cfb369aa29d3bbfc7b932e696","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"951d2f7dd3a98eafdbdf51d04d7b760f16d4ae8cfb369aa29d3bbfc7b932e696","first_computed_at":"2026-07-05T05:55:55.854564Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T05:55:55.854564Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"LRW+BYx2xCfkoi4in2bfsxvgsAfk8SWeySxAn72im1ZEe8iD5D62yJDO97PSwLGDtB/Mmz4eosR4KS6kkXm4Cg==","signature_status":"signed_v1","signed_at":"2026-07-05T05:55:55.855064Z","signed_message":"canonical_sha256_bytes"},"source_id":"2105.06222","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:7bf5470d43334901d164923d5f8805e58ba3bb63a834f7c3420bc8bfac44cf55","sha256:662864c91e996c8d48ca89687f7b95ea3fb6341a314720bcd0a17afca8bad9fe"],"state_sha256":"c6d2059774587101a13c9711e3043376095ed048653e35954944745c244e8d3c"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"QsY0lmS+qIh8PZc/w45x8Mcz+vrL922aCNJULdoQPILDf4Zkn505DVRv3eMfSmuwcH3TDI2Q/FH4r0DUHa5SBw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-04T10:49:54.800260Z","bundle_sha256":"8c9247311a513f154e69e1eb90213e14b12e432ea09aaa5cbfecf38d542efc14"}}