{"id":"W2056176287","doi":"10.1110/ps.073105408","title":"Side chain burial and hydrophobic core packing in protein folding transition states","year":2008,"lang":"en","type":"article","venue":"Protein Science","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"","keywords":"Side chain; Folding (DSP implementation); Folding funnel; Protein folding; Contact order; Lattice protein; Chemistry; Phi value analysis; Native state; Chemical physics; Globular protein; Downhill folding; Hydrophobic effect; Crystallography; Chain (unit); Limiting; Biophysics; Physics; Biology; Biochemistry; Organic chemistry; Polymer","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0004260296,0.000141141,0.0001240581,0.0001017574,0.0002414595,0.00003568862,0.000203522,0.00008748087,0.000002738895],"category_scores_gemma":[0.0001005046,0.000131675,0.00002770879,0.0003138016,0.0004993988,0.00002270909,0.00009535226,0.0001127111,0.000001197676],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002898193,"about_ca_system_score_gemma":0.0001471826,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001042194,"about_ca_topic_score_gemma":0.0000538826,"domain_scores_codex":[0.9987246,0.00003110362,0.0001853236,0.0004707212,0.0002398855,0.00034839],"domain_scores_gemma":[0.9995782,0.00000451387,0.00006553392,0.0002113019,0.00005415534,0.0000862469],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00006517721,0.00001206494,0.0002671994,0.00001702248,0.000001779207,0.00001991554,0.0003006683,0.0001330971,0.997304,0.0001707092,0.000001525231,0.001706856],"study_design_scores_gemma":[0.0006699443,0.0002926932,0.001520104,0.00007700744,0.000002338192,0.00008616978,0.00008096335,0.004367502,0.9885402,0.00391874,0.0001674195,0.0002769683],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9951642,0.0003520294,0.003422371,0.0001142246,0.00004149022,0.0007417743,0.000005741761,0.00001498126,0.0001431709],"genre_scores_gemma":[0.9960775,0.00004424547,0.003542572,0.00007918717,0.00009339728,0.00009063186,0.0000115919,0.0000115702,0.00004928306],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.008763837,"threshold_uncertainty_score":0.5369551,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0112129525072155,"score_gpt":0.2406726126486498,"score_spread":0.2294596601414343,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}