{"id":"W4412933707","doi":"10.1093/genetics/iyaf153","title":"Residues neighboring an SH3-binding motif participate in the interaction in vivo","year":2025,"lang":"en","type":"article","venue":"Genetics","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Centre hospitalier de l'Université Laval; Centre hospitalier universitaire de Québec; Université Laval","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada; University of California, San Francisco; Lawyers Trust Fund of Illinois; Canadian Institutes of Health Research; Alliance de recherche numérique du Canada; Human Frontier Science Program","keywords":"SH3 domain; Binding site; Biology; Mutant; Plasma protein binding; Sequence motif; Saccharomyces cerevisiae; Binding selectivity; Complementation; Protein-fragment complementation assay; Protein–protein interaction; DNA-binding protein; Genetics; Structural motif; Transcription factor; Cell biology; Biochemistry; Kinase; DNA; Gene; Proto-oncogene tyrosine-protein kinase Src","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":[0.0003615812,0.00009598948,0.00008526731,0.00007466095,0.0000461587,0.00004008273,0.0002111521,0.0000965842,0.00001464708],"category_scores_gemma":[0.00005174127,0.0000812244,0.0000284519,0.0001382757,0.00001801086,0.000004251391,0.00005671792,0.00008184292,0.000003378134],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000145546,"about_ca_system_score_gemma":0.00002747662,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003793124,"about_ca_topic_score_gemma":0.0008123288,"domain_scores_codex":[0.9991554,0.0001566812,0.0001895663,0.0002201378,0.00007449593,0.0002037463],"domain_scores_gemma":[0.9996028,0.00002077082,0.00003666234,0.0003027176,0.00001599635,0.00002107021],"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":[0.00003723068,0.00006256862,0.01245223,0.00001137275,0.000007620284,0.000004632476,0.0003070158,0.0006409427,0.9782529,0.0002491037,0.00008879972,0.00788554],"study_design_scores_gemma":[0.0001968341,0.0001198512,0.006767535,0.00004223431,0.000007966415,0.000002163012,0.0006749463,0.00033475,0.9854258,0.0007596041,0.005565251,0.000103006],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.996886,0.000315963,0.0008268034,0.0001817117,0.0001646547,0.0001659452,0.000002602589,0.000005457914,0.001450905],"genre_scores_gemma":[0.9985974,0.0001935965,0.0006775329,0.0001883502,0.00007898534,0.0000475384,0.000007265724,0.000009249541,0.0002000236],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.007782534,"threshold_uncertainty_score":0.3312235,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02757336704055047,"score_gpt":0.3065703462483766,"score_spread":0.2789969792078261,"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."}}