{"id":"W2056710036","doi":"10.1371/journal.ppat.1003342","title":"Broadly Neutralizing Antibody PGT121 Allosterically Modulates CD4 Binding via Recognition of the HIV-1 gp120 V3 Base and Multiple Surrounding Glycans","year":2013,"lang":"en","type":"article","venue":"PLoS Pathogens","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":298,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"SLAC National Accelerator Laboratory; Biological and Environmental Research; National Center for Research Resources; National Institute of Allergy and Infectious Diseases; National Institute of Mental Health; National Heart, Lung, and Blood Institute; National Institute on Aging; Basic Energy Sciences; University of California, San Diego; Center for AIDS Research, University of Washington; Office of Science; Nederlandse Organisatie voor Wetenschappelijk Onderzoek; National Institute on Drug Abuse; Engineering and Physical Sciences Research Council; Canadian Institutes of Health Research; National Cancer Institute; Ragon Institute of MGH, MIT and Harvard; National Institutes of Health; National Institute of General Medical Sciences; International AIDS Vaccine Initiative; U.S. Department of Energy","keywords":"Glycan; Paratope; Epitope; Alanine scanning; Allosteric regulation; Antibody; Neutralization; Trimer; Chemistry; Immunoglobulin Fab Fragments; Binding site; Glycobiology; Mutagenesis; Biology; Biochemistry; Immunoglobulin light chain; Complementarity determining region; Receptor; Glycoprotein; Mutation; Genetics","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.000143421,0.0001906023,0.0002685279,0.000103243,0.0002949867,0.00003476021,0.0001567956,0.0001421454,0.0002378265],"category_scores_gemma":[0.0001489601,0.0001350215,0.0001037911,0.000168469,0.0001863085,0.0001577501,0.0001375224,0.0002120062,0.0008883966],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004654817,"about_ca_system_score_gemma":0.00003080922,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003004529,"about_ca_topic_score_gemma":0.00003111057,"domain_scores_codex":[0.9985747,0.0002873338,0.0002843771,0.0003165913,0.00007074274,0.0004663038],"domain_scores_gemma":[0.9991778,0.0002668189,0.0001215616,0.0002663024,0.000106859,0.0000607031],"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":[0.00003746646,0.0001879496,0.1238173,0.00003850354,0.000171903,0.000009344011,0.0004007203,0.00000252556,0.8722739,0.000003672622,0.00008911431,0.002967546],"study_design_scores_gemma":[0.003170273,0.0004979675,0.1826492,0.000323065,0.0002200506,0.0001418194,0.0007190363,0.0005301866,0.8106444,0.000140948,0.0005008747,0.0004621829],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9977661,0.0003561628,0.0001146738,0.000276992,0.0001395026,0.000577241,0.0005575893,0.00005906301,0.0001526429],"genre_scores_gemma":[0.9985418,0.0001091907,0.000402675,0.00004301528,0.00002170056,0.00003833817,0.0005461787,0.00002959374,0.0002674872],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06162953,"threshold_uncertainty_score":0.9998896,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02806873490132856,"score_gpt":0.2444970156003854,"score_spread":0.2164282806990569,"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."}}