{"id":"W2081076958","doi":"10.1016/j.tibs.2010.12.001","title":"Evolving specificity from variability for protein interaction domains","year":2011,"lang":"en","type":"article","venue":"Trends in Biochemical Sciences","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":44,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto; Western University","funders":"Canadian Institutes of Health Research; Canada Research Chairs; Ontario Genomics Institute; Genome Canada","keywords":"PDZ domain; Homology (biology); Computational biology; Binding site; SH3 domain; ENCODE; Scaffold protein; Biology; Protein–protein interaction; Phosphotyrosine-binding domain; Ligand (biochemistry); Plasma protein binding; SH2 domain; Phosphorylation; Genetics; Proto-oncogene tyrosine-protein kinase Src; Amino acid; Biochemistry; Signal transduction; 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":[0.0003352902,0.0001152591,0.0001098179,0.00005108,0.00007158501,0.0000217297,0.0002885174,0.0001422791,0.000122179],"category_scores_gemma":[0.0001811636,0.00009526128,0.00006810449,0.0002063179,0.0002550709,0.00001003393,0.00009365124,0.00007997545,0.000001348797],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002765295,"about_ca_system_score_gemma":0.00002557266,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000186444,"about_ca_topic_score_gemma":0.00008753962,"domain_scores_codex":[0.9989617,0.00003864632,0.0001898175,0.0004736292,0.0001068125,0.0002293771],"domain_scores_gemma":[0.9996291,0.00001843962,0.00006507705,0.0002035743,0.00003024446,0.00005351745],"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":[0.0001077727,0.00007145889,0.005467952,0.000004170941,0.000006874508,4.108354e-7,0.00006618894,0.000001984624,0.9867244,0.0006913814,0.0002224999,0.006634871],"study_design_scores_gemma":[0.0003054785,0.0001930854,0.01480104,0.00001560273,0.000005901316,0.000001559438,0.00006071927,0.0006121116,0.9661739,0.01673463,0.0008898256,0.0002060739],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9861404,0.00007494012,0.005902491,0.00005090567,0.000124711,0.0001442656,0.00003467391,0.00001260345,0.007515048],"genre_scores_gemma":[0.9720362,0.00000338705,0.0275963,0.00003807852,0.0001513945,0.00004223804,0.00006211823,0.000005123961,0.00006517813],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02169381,"threshold_uncertainty_score":0.3884642,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03009346779525637,"score_gpt":0.2942812646604154,"score_spread":0.264187796865159,"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."}}