{"id":"W2981795052","doi":"10.1002/pro.3759","title":"Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities","year":2019,"lang":"en","type":"article","venue":"Protein Science","topic":"Hippo pathway signaling and YAP/TAZ","field":"Biochemistry, Genetics and Molecular Biology","cited_by":12,"is_retracted":false,"has_abstract":true,"ca_institutions":"Lunenfeld-Tanenbaum Research Institute; Mount Sinai Hospital; University of Toronto","funders":"Canadian Institutes of Health Research","keywords":"PDZ domain; Biology; Mutation; Peptide; Ligand (biochemistry); Genetics; Computational biology; Biochemistry; Gene; Receptor","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0003555159,0.0001170164,0.0002135071,0.0001800995,0.00009815657,0.00001833448,0.0004145546,0.00005051156,0.0000768858],"category_scores_gemma":[0.00003152558,0.0001053126,0.0001299131,0.000647022,0.0003807805,0.000008071797,0.0002099568,0.00006125626,0.00003326189],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002411519,"about_ca_system_score_gemma":0.0001329244,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007235574,"about_ca_topic_score_gemma":0.000005123774,"domain_scores_codex":[0.9986152,0.00005945327,0.0002218242,0.0004335523,0.0004015537,0.0002684192],"domain_scores_gemma":[0.9991407,0.00001492559,0.000118081,0.0004172337,0.0002193697,0.00008973802],"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":[0.00001513941,0.00002259362,0.02018513,0.00001123085,0.000101071,9.55746e-7,0.0001572732,0.0005594476,0.9783198,0.0002932042,0.00001165605,0.0003225598],"study_design_scores_gemma":[0.0003535079,0.0003210434,0.04078167,0.00002636648,0.0001000026,0.000001256098,0.0004748594,0.0005075249,0.9474327,0.0005970426,0.009108968,0.0002950537],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968827,0.0004486672,0.001330732,0.00003871423,0.00007257718,0.0002641066,0.00007745883,0.000009364859,0.0008757173],"genre_scores_gemma":[0.9970105,0.00001370786,0.002427393,0.00004159138,0.00007685619,0.00001306942,0.00005991078,0.000006100171,0.0003508465],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03088703,"threshold_uncertainty_score":0.4294523,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02279499840014578,"score_gpt":0.2783194329604177,"score_spread":0.2555244345602719,"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."}}