{"id":"W2095368311","doi":"10.1038/ncomms3037","title":"Antagonism between binding site affinity and conformational dynamics tunes alternative cis-interactions within Shp2","year":2013,"lang":"en","type":"article","venue":"Nature Communications","topic":"Protein Tyrosine Phosphatases","field":"Biochemistry, Genetics and Molecular Biology","cited_by":46,"is_retracted":false,"has_abstract":false,"ca_institutions":"Princess Margaret Cancer Centre; University Health Network; University of Toronto; Ontario Institute for Cancer Research","funders":"Division of Chemical, Bioengineering, Environmental, and Transport Systems; National Institute of General Medical Sciences; National Heart, Lung, and Blood Institute; Princess Margaret Hospital Foundation; National Cancer Institute; National Science Foundation; National Institutes of Health; Harvard University","keywords":"GRB2; SH2 domain; Modular design; Sequence (biology); Signal transducing adaptor protein; Phosphotyrosine-binding domain; Binding site; Stereochemistry; Protein structure; Protein tyrosine phosphatase; Tyrosine; Computational biology; Chemistry; Biology; Biochemistry; Signal transduction; Computer science","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":[0.0001213292,0.0001300514,0.0001109235,0.00006400309,0.000349693,0.00008998679,0.0004894483,0.0001643525,0.0000176359],"category_scores_gemma":[0.0002071964,0.0001284416,0.00004151302,0.0001002955,0.0001770797,0.0000417525,0.000521857,0.0004842313,0.00004377267],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003232876,"about_ca_system_score_gemma":0.00005031655,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001324903,"about_ca_topic_score_gemma":0.000462543,"domain_scores_codex":[0.9993044,0.00007473463,0.0002203343,0.000166523,0.0001010706,0.0001329931],"domain_scores_gemma":[0.9986679,0.0001121756,0.0001625647,0.0007766932,0.0002070759,0.00007357632],"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":[0.0001289611,0.0007070293,0.1434258,0.0001251107,0.001401514,0.000002803287,0.002020024,0.0002259088,0.460376,0.3205014,0.04924131,0.02184411],"study_design_scores_gemma":[0.001807316,0.0003111241,0.09200791,0.0001302579,0.0001749245,0.00009782644,0.0009032984,0.01349274,0.7904308,0.004735885,0.09462278,0.001285144],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9725367,0.01019273,0.002560999,0.007290289,0.0003568504,0.0009328326,0.003208855,0.0000765575,0.002844137],"genre_scores_gemma":[0.9857417,0.0004218379,0.006254818,0.0002711962,0.000088272,0.00008444719,0.006979469,0.00001390416,0.0001443541],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3300548,"threshold_uncertainty_score":0.5237697,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01579504773477675,"score_gpt":0.295721400783082,"score_spread":0.2799263530483052,"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."}}