{"id":"W2806365862","doi":"10.1186/s12900-018-0086-3","title":"Functional insights from proteome-wide structural modeling of Treponema pallidum subspecies pallidum, the causative agent of syphilis","year":2018,"lang":"en","type":"article","venue":"BMC Structural Biology","topic":"Syphilis Diagnosis and Treatment","field":"Medicine","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Victoria","funders":"National Institute of Allergy and Infectious Diseases; National Institutes of Health","keywords":"Treponema; Proteome; Virulence; Biology; Computational biology; Genetics; Syphilis; Genome; Gene; Microbiology; Virology","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":[0.00007128298,0.0003025807,0.0006455387,0.0001104201,0.0001546334,0.000009615879,0.0001690964,0.0001815101,0.0007870914],"category_scores_gemma":[0.0002563989,0.0001597051,0.0002400199,0.000192835,0.0006825215,0.00006042607,0.00010688,0.000155418,0.00001030824],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00009655997,"about_ca_system_score_gemma":0.0001232386,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001015328,"about_ca_topic_score_gemma":0.001105749,"domain_scores_codex":[0.9981796,0.0001609312,0.0006577321,0.000454142,0.000267659,0.0002800079],"domain_scores_gemma":[0.9982271,0.000447966,0.0003457015,0.0004775084,0.0004098505,0.00009187253],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.001383261,0.00008088654,0.9426115,0.00008520262,0.001198807,0.00001246001,0.003402885,0.0003692965,0.04215361,0.006797547,0.0001837661,0.001720854],"study_design_scores_gemma":[0.001765916,0.0008846881,0.9300559,0.00007565215,0.0002325855,0.00002497978,0.000661318,0.002950656,0.05132608,0.01174015,0.0001001461,0.0001819494],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.996456,0.00112067,0.0001701964,0.0004486028,0.0005839228,0.0007695114,0.0001997927,0.00002822638,0.0002231308],"genre_scores_gemma":[0.9975356,0.00004397129,0.001258075,0.0001322225,0.0005923837,0.00006028567,0.000317392,0.00001793042,0.00004215881],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01255556,"threshold_uncertainty_score":0.8618099,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06668022112420356,"score_gpt":0.2978571101213261,"score_spread":0.2311768889971225,"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."}}