{"id":"W2114884926","doi":"10.1093/oxfordjournals.molbev.a004009","title":"The Pattern of Amino Acid Replacements in α/β-Barrels","year":2002,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":66,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"","keywords":"Biology; Active site; Amino acid; Phylogenetic tree; Molecular evolution; Protein structure; Protein secondary structure; Binding site; Protein engineering; Evolutionary biology; Enzyme; Biochemistry; Stereochemistry; Chemistry","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":[0.0001215711,0.00008079466,0.00007923535,0.00002622551,0.00005762012,0.000003978896,0.00008917039,0.0001495893,0.000003727207],"category_scores_gemma":[0.00004441874,0.000061474,0.00003129238,0.00005134587,0.0001347204,0.000001691748,0.00006716697,0.0000626194,0.000002115778],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008554314,"about_ca_system_score_gemma":0.000006569285,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003244327,"about_ca_topic_score_gemma":0.0000483889,"domain_scores_codex":[0.9994037,0.00007727319,0.0001472009,0.0001846765,0.00003166893,0.0001554806],"domain_scores_gemma":[0.9996948,0.000005397961,0.00005709572,0.0002019394,0.00002272864,0.00001801673],"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":[0.00003058625,0.00001845063,0.04899179,0.000006543963,0.0000253562,0.000001254618,0.00002148715,0.00001476328,0.9360479,0.000855462,0.00007351444,0.01391288],"study_design_scores_gemma":[0.002616583,0.001276747,0.1253125,0.00004017707,0.00004319822,0.00007348827,0.0001091498,0.002630161,0.8475921,0.009192294,0.01057198,0.000541573],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9665878,0.008998457,0.02373674,0.0001308033,0.0000968642,0.0001211503,0.000007590868,0.000003520631,0.000317048],"genre_scores_gemma":[0.99932,0.0003342768,0.0001009331,0.0000859771,0.00001850045,0.00001276215,0.00003634464,0.000005181597,0.00008597312],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.08845577,"threshold_uncertainty_score":0.2506837,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.004258058881162393,"score_gpt":0.2297438771010678,"score_spread":0.2254858182199053,"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."}}