{"id":"W2047995544","doi":"10.1074/jbc.m109.028431","title":"Structural, Functional, and Bioinformatic Studies Demonstrate the Crucial Role of an Extended Peptide Binding Site for the SH3 Domain of Yeast Abp1p","year":2009,"lang":"en","type":"article","venue":"Journal of Biological Chemistry","topic":"Biochemical and Structural Characterization","field":"Biochemistry, Genetics and Molecular Biology","cited_by":49,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; University of Toronto","funders":"","keywords":"SH3 domain; Peptide; Binding site; Mutagenesis; Plasma protein binding; Biology; Yeast; Protein–protein interaction; Biochemistry; Binding domain; Function (biology); Saccharomyces cerevisiae; Conserved sequence; Peptide sequence; Computational biology; Biophysics; Cell biology; Proto-oncogene tyrosine-protein kinase Src; Kinase; Mutation; 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":[0.0002230218,0.0001191171,0.0002139279,0.00001060135,0.00009460733,0.00001429031,0.0001681143,0.0001327792,0.000009078952],"category_scores_gemma":[0.000166451,0.00005465596,0.0001247077,0.00005463817,0.0002639444,0.00001179823,0.00004051827,0.0001128961,7.846259e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006972845,"about_ca_system_score_gemma":0.0000254708,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":5.24515e-7,"about_ca_topic_score_gemma":3.234061e-7,"domain_scores_codex":[0.9992223,0.00002355655,0.0004245778,0.0001042402,0.0001079944,0.0001172816],"domain_scores_gemma":[0.9991592,0.00004972851,0.0004562072,0.0001087159,0.0001792837,0.00004693603],"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":[0.000334932,0.00001370883,0.0002875142,0.00002759401,0.00006656234,2.972173e-7,0.00006168686,0.000006817478,0.9947085,0.00001150138,0.00003892967,0.004441943],"study_design_scores_gemma":[0.0004178382,0.0004476701,0.02428757,0.00002865487,0.00003920703,0.0001214725,0.0008114754,0.0000974231,0.9720657,0.001422396,0.0001699756,0.00009060036],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9978922,0.001600999,0.00008710965,0.0002115011,0.00004055507,0.00008788282,0.0000552942,0.000001961545,0.00002250919],"genre_scores_gemma":[0.9986537,0.0003531464,0.0005868186,0.0000697688,0.0002726181,0.000001825366,0.00004804276,0.000002913269,0.00001116954],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02400006,"threshold_uncertainty_score":0.2228805,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02111542829161522,"score_gpt":0.2586039234848241,"score_spread":0.2374884951932089,"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."}}