{"id":"W3029437323","doi":"10.1128/mbio.00280-20","title":"The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site","year":2020,"lang":"en","type":"article","venue":"mBio","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; McGill University; Centre Hospitalier de l’Université de Montréal","funders":"National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; Canadian Institutes of Health Research; Government of Canada; National Institutes of Health; University of Iowa; Canada Research Chairs; Deutsche Forschungsgemeinschaft","keywords":"Human immunodeficiency virus (HIV); Virology; Binding site; Domain (mathematical analysis); Biology; Chemistry; Computational biology; Biophysics; Genetics","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0004026639,0.0001092445,0.0001276625,0.00001098561,0.0009604854,0.00006243848,0.0002415204,0.00007024017,0.0002171503],"category_scores_gemma":[0.0001092934,0.00004129403,0.0000612394,0.00009600745,0.0006855693,0.00003019709,0.0001923333,0.0003050231,0.003576553],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001685163,"about_ca_system_score_gemma":0.00002636356,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001311718,"about_ca_topic_score_gemma":0.0001660273,"domain_scores_codex":[0.9989421,0.000414328,0.0001128201,0.0001769106,0.00004033144,0.0003134905],"domain_scores_gemma":[0.9991684,0.0005668853,0.00003778861,0.0001805857,0.00001725834,0.00002906719],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.004340461,0.0003193309,0.05702576,0.00005663898,0.00296094,0.0001240389,0.04271386,0.000006330369,0.382643,0.0227888,0.3957691,0.0912517],"study_design_scores_gemma":[0.003243109,0.0001381744,0.00919126,0.00000840817,0.0000464341,0.00003367646,0.001150698,0.00001220756,0.005678485,0.0003692089,0.9800128,0.0001155812],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9287878,0.007816485,0.00003202167,0.06004586,0.0001181062,0.0004582945,0.0002320798,0.00003792383,0.002471461],"genre_scores_gemma":[0.9960946,0.0003803934,0.000009775555,0.00077041,0.00005477607,0.00004727848,0.00007542864,0.000007769305,0.00255953],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5842436,"threshold_uncertainty_score":0.9971993,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01283374980263739,"score_gpt":0.2306569352679783,"score_spread":0.2178231854653409,"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."}}