{"id":"W2068757386","doi":"10.1371/journal.ppat.1004767","title":"Comprehensive Antigenic Map of a Cleaved Soluble HIV-1 Envelope Trimer","year":2015,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":103,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; SickKids Foundation; University of Toronto","funders":"National Institute of Allergy and Infectious Diseases; National Center for Research Resources; National Institute of General Medical Sciences; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; Aids Fonds; National Institutes of Health; International AIDS Vaccine Initiative","keywords":"Epitope; Trimer; Gp41; Antigen; Subdominant; Epitope mapping; Binding site; Antibody; Plasma protein binding; Biology; Virology; Chemistry; Cell biology; Biochemistry; Immunology","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0001012299,0.0001542817,0.0003337733,0.0001003171,0.00007824595,0.000006152864,0.0001753289,0.0001394614,0.0006727687],"category_scores_gemma":[0.00005131106,0.000126777,0.0001074114,0.0001004141,0.0001831383,0.00004353813,0.0001102895,0.0001595114,0.01352526],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004110827,"about_ca_system_score_gemma":0.0002044107,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004331688,"about_ca_topic_score_gemma":0.000006330207,"domain_scores_codex":[0.9988061,0.0002043128,0.0002380784,0.0002506582,0.00007303578,0.0004278496],"domain_scores_gemma":[0.9992024,0.00008476417,0.00007532758,0.0003288905,0.0002264812,0.00008208208],"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":[0.0004178123,0.0007946868,0.02213024,0.00004336659,0.0008287391,0.00007785074,0.001217378,0.000003141054,0.9312904,0.0000921633,0.04152519,0.001579065],"study_design_scores_gemma":[0.007718767,0.001159345,0.02298863,0.00005091597,0.0001916628,0.00006035354,0.001194093,0.000008947432,0.6855817,0.0001532861,0.2805072,0.0003850436],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9904186,0.005239399,0.00005487088,0.0003156009,0.0002999115,0.0004332383,0.0004162743,0.00006523952,0.002756843],"genre_scores_gemma":[0.9911352,0.00007011709,0.000482977,0.00005329045,0.00002300247,0.00003189071,0.000467872,0.00001932886,0.007716333],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2457086,"threshold_uncertainty_score":0.9872428,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06476474176685411,"score_gpt":0.2760494437054538,"score_spread":0.2112847019385997,"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."}}