{"paper":{"title":"When Does Structure Help? The Information Bonus of AlphaFold2 Representations over Protein Language Models","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.CE","authors_text":"Kargi Chauhan","submitted_at":"2026-06-02T21:26:09Z","abstract_excerpt":"AI scientist systems increasingly choose biological foundation models before they choose experiments. In protein pipelines, this creates a concrete engineering and scientific question: when is the cost of structural inference worth paying over a cheaper sequence-only model? We introduce the information bonus (IB), a task-level metric that measures the linearly accessible advantage of frozen single-sequence AlphaFold2 Evoformer representations over frozen ESM-2 embeddings under protein-level cross-validation. Across binding affinity regression (PDBbind, n=5,680), conformational flexibility (ATL"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.04228","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":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.04228/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"}