{"id":"W2144811782","doi":"10.1186/1471-2105-12-225","title":"Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences","year":2011,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":49,"is_retracted":false,"has_abstract":true,"ca_institutions":"Carleton University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Binding site; Proteome; Computational biology; Protein–protein interaction; Plasma protein binding; Sequence motif; Protein Array Analysis; Binding domain; Biology; Sequence (biology); Bioinformatics; DNA microarray; Genetics; Biochemistry; Gene","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":[0.0002585367,0.0002090946,0.0001645591,0.00009382935,0.000240642,0.0001261311,0.000139755,0.0001511004,0.000006060362],"category_scores_gemma":[0.0000561884,0.0001921939,0.00009605178,0.0000893659,0.00009249545,0.0001065486,0.0001546209,0.0001203905,0.000006384651],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003277103,"about_ca_system_score_gemma":0.00008501629,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004219661,"about_ca_topic_score_gemma":0.00006583792,"domain_scores_codex":[0.9988772,0.00001114006,0.0005189759,0.0001743591,0.0001041644,0.0003141574],"domain_scores_gemma":[0.999253,0.00001057543,0.0003028017,0.0002737639,0.00006716575,0.00009272563],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0004601653,0.0001640961,0.008369904,0.001500081,0.0002973243,8.518961e-7,0.003029552,0.002049373,0.9739837,0.002728748,0.0006351841,0.006781021],"study_design_scores_gemma":[0.002160261,0.0006680054,0.001012591,0.000750336,0.0001583577,0.0001160263,0.002949283,0.8605511,0.1225999,0.0008341155,0.007117078,0.001082917],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.4664502,0.00005158973,0.5319445,0.000005297223,0.0001464654,0.0005643824,0.0002434426,0.00001845506,0.0005756001],"genre_scores_gemma":[0.6163526,0.00001565722,0.3825448,0.0001003161,0.000249946,0.00007665013,0.000230585,0.00003027753,0.0003992223],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.8585018,"threshold_uncertainty_score":0.7837439,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04587082751055672,"score_gpt":0.2596847144328296,"score_spread":0.2138138869222729,"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."}}