{"id":"W2085075228","doi":"10.1021/bi050293e","title":"Mutual Information in Protein Multiple Sequence Alignments Reveals Two Classes of Coevolving Positions","year":2005,"lang":"en","type":"article","venue":"Biochemistry","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":256,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"","keywords":"Coevolution; Multiple sequence alignment; Set (abstract data type); Sequence (biology); Sequence alignment; Function (biology); Biology; Computational biology; Protein structure; Protein family; Mutual information; Computer science; Genetics; Evolutionary biology; Peptide sequence; Artificial intelligence; Gene","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":[0.00008975748,0.00011956,0.0001080235,0.00003101432,0.00003377735,0.00001397574,0.0001559928,0.0001427711,0.00001067002],"category_scores_gemma":[0.0001359195,0.0001263471,0.00004618667,0.0000811267,0.00006328543,0.00001765992,0.00007750118,0.00007228607,0.000004972244],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004512951,"about_ca_system_score_gemma":0.00008291263,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002878879,"about_ca_topic_score_gemma":0.00001843438,"domain_scores_codex":[0.9992355,0.00001753388,0.0002904847,0.0001612001,0.0001227559,0.00017258],"domain_scores_gemma":[0.9994844,0.00000675964,0.0001328035,0.0002563027,0.00007165469,0.0000480815],"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":[0.00003428905,0.00002990524,0.002439745,0.00004883987,0.00001073434,6.541716e-7,0.00003020046,0.0001505872,0.9959793,0.00004171489,0.0001671881,0.001066813],"study_design_scores_gemma":[0.0005607277,0.00003844776,0.0006930953,0.0000590464,0.000004829211,0.00001119625,0.00005101012,0.00076789,0.9966929,0.00006692608,0.0009096328,0.0001443054],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9974191,0.0001641551,0.0009811734,0.00008122897,0.00001939761,0.0002130599,0.0001057648,0.000009963312,0.001006193],"genre_scores_gemma":[0.9927999,0.00001772373,0.00633405,0.0001105653,0.00009532847,0.00003930897,0.0004236235,0.000007469743,0.0001720415],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.005352877,"threshold_uncertainty_score":0.5152287,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007279509674066808,"score_gpt":0.2557520582365386,"score_spread":0.2484725485624718,"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."}}