{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00007094596,0.0002446194,0.0002070233,0.00009583537,0.0001253854,0.0002930888,0.0002695108,0.0002538556,0.001011957],"category_scores_gemma":[0.000109393,0.00007985023,0.000166748,0.0001103825,0.000173618,0.0001300053,0.0001825065,0.0004436987,0.0002985935],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000353972,"about_ca_system_score_gemma":0.000130682,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000407015,"about_ca_topic_score_gemma":0.0004693048,"domain_scores_codex":[0.9999009,0.00001041603,0.000003706284,0.00001805012,0.00003603266,0.00003092353],"domain_scores_gemma":[0.9999604,0.000005598321,0.000009298116,0.000004314951,0.000003900584,0.00001648465],"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":[0.00009940766,0.00004619136,0.000499295,0.00001250758,0.000003736253,0.00006284499,0.000008796425,0.0002583977,0.995125,0.0000621358,0.00007234863,0.003749414],"study_design_scores_gemma":[0.00005733128,0.001088996,0.009537983,0.000004003458,0.0000234953,0.001277579,0.00002439907,0.003098796,0.9799331,0.00008120521,0.004865323,0.00000770688],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9971982,0.0002750476,0.0007751535,0.00004425191,0.000005635934,0.00002137661,0.00005777044,0.00004459375,0.001577999],"genre_scores_gemma":[0.9972298,0.0002918575,0.001105334,0.00008773419,0.000007750076,0.00001359476,0.0002175658,0.000009560725,0.001036832],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001011957,"threshold_uncertainty_score":0.003385365,"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."}}