{"record":{"author":{"account_ref":null,"orcid":null},"builds_on":[],"content_schema":"pubphys.content.revision/1","content_sha256":"a038b2aa4903f271b0a14cff680f77ee311850cb721e9d7c0e89dde6ae800187","created":"2026-10-03T07:17:57Z","files":[],"origin":{"assisted_by":[],"kind":"seed"},"parents":["5475cf5dc5b1a72283d26dc95dc6e00d7ea4e00096a7c6492e409a1816eeb011"],"salt":"e7a9889456fe910799d6ebea82aac689f6b72696dd80444ef72475e19692345e","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":"1","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":null,"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 $\\operatorname{ln} k_f$.","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":"d70805bb63f25bf8902aa9ee3d70d8c036572d9638addfbea7d1b841f5ab7b17"},"attested":{"attestation":{"batch":null,"client_id":null,"id_token_sha256":null,"kind":"platform"},"record_hash":"034d04f3cc771a438d8414e0346e24e203583fc394f50573fde94b13fe643248","schema":"pubphys.attested/1"},"envelope":{"attested_hash":"a24ec47b6240bf010cc0d07278cbc9dbf808831c056b24a880d7eca2b770ec2c","platform_signature":{"key_id":"c6afc19b31429869751f06879c75cd64ea92654423d15b44be775bf1310a60da","sig":"JWp4W9vJSK393bStl0nEZqkDsTb5cpjb7m2zmu1tl8CAUJOvDOAA8YWI9RBDEcxHx8ox9lFKDjGPcdTuJjd9DQ"},"schema":"pubphys.envelope/1"},"record_hash":"034d04f3cc771a438d8414e0346e24e203583fc394f50573fde94b13fe643248","leaf_index":831}