{"record":{"author":{"account_ref":null,"orcid":null},"builds_on":[],"content_schema":"pubphys.content.revision/1","content_sha256":"fd8c614793c8646426c69b675e5b5155c3d069fc040201e52e3a6a4096c68f8c","created":"2026-10-15T23:43:22Z","files":[],"origin":{"assisted_by":[],"kind":"seed"},"parents":["034d04f3cc771a438d8414e0346e24e203583fc394f50573fde94b13fe643248","ce59fb6cd812fc05906d0c60a71c75ea22bc686bcf38e7c3ef7010834d98ee7b"],"salt":"49168c71908a6ffcccf32318da03888c9c1b496bcf61f3af223e94b6f0c2a1fe","schema":"pubphys.record/2","site":"pubphys.com","target":null,"type":"revision"},"content":{"answer_type":"value","assisted_by":[],"external_id":"bio.protein-folding.sequence-to-rate","kind":"well-posed","literature_status":"open","n":"2","parents":[],"plain":"Small proteins fold at rates that differ by roughly a factor of a hundred million, and sequence-based formulas reproduce the trend only on proteins they were fitted to. The goal is a sequence-only predictor whose accuracy holds on proteins it has never seen.","posed_since":"1998","precise":"For single-domain two-state proteins of 40 to 150 residues in water near $298\\,\\mathrm{K}$, predict $\\ln k_f$ ($k_f = \\text{folding rate in } \\mathrm{s}^{-1}$) from sequence alone; measured rates span approximately 8 decades, topology measures such as relative contact order correlate with $\\ln k_f$ at $r \\sim 0.8$ when the native structure is given, and sequence-only fits reach $r \\sim 0.8$ in-sample (Ivankov and Finkelstein, 2004). An answer is a method with a stated root-mean-square error, target below 1 unit of $\\ln k_f$, on a blind set of proteins with measured rates that are absent from its training data.","problem_ref":"034d04f3cc771a438d8414e0346e24e203583fc394f50573fde94b13fe643248","references":"","settled_by":"A blind test on newly measured folding rates of proteins absent from any training data, scored by root-mean-square error in $\\ln k_f$.","status_note":"Structure-prediction networks (AlphaFold 2 in 2021 and successors) give native structures, but no blind sequence-to-rate benchmark at this accuracy is known to this survey as of 2026.","title":"Predict a protein's folding rate from its sequence alone","topic_ref":null},"attested":{"attestation":{"batch":null,"client_id":null,"id_token_sha256":null,"kind":"platform"},"record_hash":"77db4b5aec660a64fa50a252edc7ce6375a396b3e295daa24f44f5fd090bff2c","schema":"pubphys.attested/1"},"envelope":{"attested_hash":"2652bd098d0c676d7e208af3445772c8817100eb4da6d61c4305217ee096792f","platform_signature":{"key_id":"c6afc19b31429869751f06879c75cd64ea92654423d15b44be775bf1310a60da","sig":"nWULtb-d_X574U85tbJR_lAZ8mYuMbb__yMgmSJCbDyTeQ-2WRcQUXvIXFF868z9I9SJeiDArDPNwzZDAS0RBQ"},"schema":"pubphys.envelope/1"},"record_hash":"77db4b5aec660a64fa50a252edc7ce6375a396b3e295daa24f44f5fd090bff2c","leaf_index":2622}