{"id":"W1970431511","doi":"10.1093/nar/gks398","title":"PepSite: prediction of peptide-binding sites from protein surfaces","year":2012,"lang":"en","type":"article","venue":"Nucleic Acids Research","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":212,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Toronto; Mount Sinai Hospital","funders":"Alexander von Humboldt-Stiftung","keywords":"Biology; Peptide; Computational biology; Plasma protein binding; Binding site; Biochemistry","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":[0.0005601567,0.0001149013,0.0001323804,0.00008367095,0.0001305398,0.00002509501,0.0002614293,0.0002234141,0.0001055341],"category_scores_gemma":[0.0002327106,0.0001039499,0.0000615619,0.0001833347,0.0001808676,0.00001564104,0.0002529209,0.000240559,0.00003841679],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002699897,"about_ca_system_score_gemma":0.00005528389,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00009767864,"about_ca_topic_score_gemma":0.0000213142,"domain_scores_codex":[0.998528,0.0001587838,0.0001922462,0.000252468,0.000426803,0.0004416761],"domain_scores_gemma":[0.9992279,0.00002660667,0.00005676679,0.000391458,0.0001758871,0.0001213338],"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":[0.00007682946,0.00004094907,0.07839454,0.00002354602,0.00003472616,7.604946e-7,0.0001391288,0.000003917466,0.9190034,0.0001303266,0.0009243807,0.00122748],"study_design_scores_gemma":[0.0003856765,0.0003239343,0.06255122,0.00003695448,0.000009910086,0.000005562997,0.0003207389,0.0001925557,0.9249916,0.0005169254,0.01051542,0.0001494645],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9946992,0.0008368696,0.0003022497,0.00005966928,0.00006760901,0.0003275138,0.0001400583,0.00001532417,0.003551523],"genre_scores_gemma":[0.9954346,0.00006067556,0.002691679,0.000008671696,0.0004041176,0.00002667054,0.0002820345,0.00002483097,0.001066736],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01584331,"threshold_uncertainty_score":0.4238954,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03361658666262007,"score_gpt":0.3127907515569329,"score_spread":0.2791741648943128,"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."}}