{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2024:M67NTWLHPXWX3JMIB5NGRVMIQW","short_pith_number":"pith:M67NTWLH","canonical_record":{"source":{"id":"2412.19812","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-10T15:41:06Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"e8137ea9ea85c2c11033ceb3e4da3553f09af3ea4b52588dc2d0dd6a6de58bc3","abstract_canon_sha256":"4c17f4ea591d607eca9851ce25de75c2bfb84e8f412419de58ff6802f6bc69d9"},"schema_version":"1.0"},"canonical_sha256":"67bed9d9677ded7da5880f5a68d5888593451381a1712c7df7446cf08aa8e1c4","source":{"kind":"arxiv","id":"2412.19812","version":2},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.19812","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"arxiv_version","alias_value":"2412.19812v2","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.19812","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_12","alias_value":"M67NTWLHPXWX","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_16","alias_value":"M67NTWLHPXWX3JMI","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_8","alias_value":"M67NTWLH","created_at":"2026-07-05T10:05:47Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2024:M67NTWLHPXWX3JMIB5NGRVMIQW","target":"record","payload":{"canonical_record":{"source":{"id":"2412.19812","kind":"arxiv","version":2},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-10T15:41:06Z","cross_cats_sorted":["cs.LG"],"title_canon_sha256":"e8137ea9ea85c2c11033ceb3e4da3553f09af3ea4b52588dc2d0dd6a6de58bc3","abstract_canon_sha256":"4c17f4ea591d607eca9851ce25de75c2bfb84e8f412419de58ff6802f6bc69d9"},"schema_version":"1.0"},"canonical_sha256":"67bed9d9677ded7da5880f5a68d5888593451381a1712c7df7446cf08aa8e1c4","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-07-05T10:05:47.528997Z","signature_b64":"DZsoI/dRvShf0P+FUVwiOiEDJrKzLYAKJ/Uz5jaTqMYk4HTdsmyJ6MYIutInssJNS0PbE/poAghIqmKqEbDVBw==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"67bed9d9677ded7da5880f5a68d5888593451381a1712c7df7446cf08aa8e1c4","last_reissued_at":"2026-07-05T10:05:47.528496Z","signature_status":"signed_v1","first_computed_at":"2026-07-05T10:05:47.528496Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2412.19812","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":"2026-07-05T10:05:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"r92u4l9liHOMo91nLK8JkT+TV+J8tStWj5r0F4Htx6dG9ab39XAkEjOLzZGo9TJpD0XZzODrOIYa9SfC7WpMDw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T10:16:40.753772Z"},"content_sha256":"2aa756c17a21361804daf149d5a9bbed32a01267a5275dca1ad6e5898f91fdf9","schema_version":"1.0","event_id":"sha256:2aa756c17a21361804daf149d5a9bbed32a01267a5275dca1ad6e5898f91fdf9"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2024:M67NTWLHPXWX3JMIB5NGRVMIQW","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Pharmacophore-guided de novo drug design with diffusion bridge","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.LG"],"primary_cat":"q-bio.BM","authors_text":"Conghao Wang, Jagath C. Rajapakse","submitted_at":"2024-12-10T15:41:06Z","abstract_excerpt":"De novo design of bioactive drug molecules with potential to treat desired biological targets is a profound task in the drug discovery process. Existing approaches tend to leverage the pocket structure of the target protein to condition the molecule generation. However, even the pocket area of the target protein may contain redundant information since not all atoms in the pocket is responsible for the interaction with the ligand. In this work, we propose PharmacoBridge, a phamacophore-guided de novo design approach to generate drug candidates inducing desired bioactivity via diffusion bridge. "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.19812","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/2412.19812/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":"2026-07-05T10:05:47Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"44z3RKDFisn9edddEXzBsaKnMYkwl1wJyLN1jnigHlut8rH1ZkV3sReUVEwXh15rFUJ7AAb8W0u33BLe3VluDw==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-08-13T10:16:40.754681Z"},"content_sha256":"00eb5f2788c14aa67b36c17d76c201f7b5bd9adeb8291f7bb4a550261eb1308e","schema_version":"1.0","event_id":"sha256:00eb5f2788c14aa67b36c17d76c201f7b5bd9adeb8291f7bb4a550261eb1308e"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/bundle.json","state_url":"https://pith.science/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/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":"2026-08-13T10:16:40Z","links":{"resolver":"https://pith.science/pith/M67NTWLHPXWX3JMIB5NGRVMIQW","bundle":"https://pith.science/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/bundle.json","state":"https://pith.science/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/state.json","well_known_bundle":"https://pith.science/.well-known/pith/M67NTWLHPXWX3JMIB5NGRVMIQW/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2024:M67NTWLHPXWX3JMIB5NGRVMIQW","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":"4c17f4ea591d607eca9851ce25de75c2bfb84e8f412419de58ff6802f6bc69d9","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-10T15:41:06Z","title_canon_sha256":"e8137ea9ea85c2c11033ceb3e4da3553f09af3ea4b52588dc2d0dd6a6de58bc3"},"schema_version":"1.0","source":{"id":"2412.19812","kind":"arxiv","version":2}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2412.19812","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"arxiv_version","alias_value":"2412.19812v2","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2412.19812","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_12","alias_value":"M67NTWLHPXWX","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_16","alias_value":"M67NTWLHPXWX3JMI","created_at":"2026-07-05T10:05:47Z"},{"alias_kind":"pith_short_8","alias_value":"M67NTWLH","created_at":"2026-07-05T10:05:47Z"}],"graph_snapshots":[{"event_id":"sha256:00eb5f2788c14aa67b36c17d76c201f7b5bd9adeb8291f7bb4a550261eb1308e","target":"graph","created_at":"2026-07-05T10:05:47Z","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/2412.19812/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"De novo design of bioactive drug molecules with potential to treat desired biological targets is a profound task in the drug discovery process. Existing approaches tend to leverage the pocket structure of the target protein to condition the molecule generation. However, even the pocket area of the target protein may contain redundant information since not all atoms in the pocket is responsible for the interaction with the ligand. In this work, we propose PharmacoBridge, a phamacophore-guided de novo design approach to generate drug candidates inducing desired bioactivity via diffusion bridge. ","authors_text":"Conghao Wang, Jagath C. Rajapakse","cross_cats":["cs.LG"],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-10T15:41:06Z","title":"Pharmacophore-guided de novo drug design with diffusion bridge"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.19812","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":"sha256:2aa756c17a21361804daf149d5a9bbed32a01267a5275dca1ad6e5898f91fdf9","target":"record","created_at":"2026-07-05T10:05:47Z","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":"4c17f4ea591d607eca9851ce25de75c2bfb84e8f412419de58ff6802f6bc69d9","cross_cats_sorted":["cs.LG"],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.BM","submitted_at":"2024-12-10T15:41:06Z","title_canon_sha256":"e8137ea9ea85c2c11033ceb3e4da3553f09af3ea4b52588dc2d0dd6a6de58bc3"},"schema_version":"1.0","source":{"id":"2412.19812","kind":"arxiv","version":2}},"canonical_sha256":"67bed9d9677ded7da5880f5a68d5888593451381a1712c7df7446cf08aa8e1c4","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"67bed9d9677ded7da5880f5a68d5888593451381a1712c7df7446cf08aa8e1c4","first_computed_at":"2026-07-05T10:05:47.528496Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-07-05T10:05:47.528496Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"DZsoI/dRvShf0P+FUVwiOiEDJrKzLYAKJ/Uz5jaTqMYk4HTdsmyJ6MYIutInssJNS0PbE/poAghIqmKqEbDVBw==","signature_status":"signed_v1","signed_at":"2026-07-05T10:05:47.528997Z","signed_message":"canonical_sha256_bytes"},"source_id":"2412.19812","source_kind":"arxiv","source_version":2}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:2aa756c17a21361804daf149d5a9bbed32a01267a5275dca1ad6e5898f91fdf9","sha256:00eb5f2788c14aa67b36c17d76c201f7b5bd9adeb8291f7bb4a550261eb1308e"],"state_sha256":"558c20e73bd4a692bcaede10dfd4623a13584c3aee157a314d49e0839b586942"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"i9XZQSRDMDuZkuO5HCHARr2EZwIWJ0jTal5voP5RRScJdz4dDqXlCfHlphXhuQQwNXTTXTWdt4bsUM387eJ7Cg==","signed_message":"bundle_sha256_bytes","signed_at":"2026-08-13T10:16:40.764859Z","bundle_sha256":"654263375682f543e781874bbef5279045f86a25235b61e21f7d9f0b7c912143"}}