{"id":"W2050372002","doi":"10.1016/j.jmb.2008.09.024","title":"Structural Details of HIV-1 Recognition by the Broadly Neutralizing Monoclonal Antibody 2F5: Epitope Conformation, Antigen-Recognition Loop Mobility, and Anion-Binding Site","year":2008,"lang":"en","type":"article","venue":"Journal of Molecular Biology","topic":"HIV Research and Treatment","field":"Immunology and Microbiology","cited_by":80,"is_retracted":false,"has_abstract":false,"ca_institutions":"Princess Margaret Cancer Centre; Canada Research Chairs; Ontario Institute for Cancer Research; University of Toronto","funders":"","keywords":"Epitope; Gp41; Paratope; Monoclonal antibody; Chemistry; V3 loop; Peptide; Linear epitope; Antibody; Neutralization; Antigen; Epitope mapping; Biophysics; Virology; Biochemistry; Biology; Virus","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":[0.0004158368,0.0001537386,0.000324517,0.0001516805,0.0002322631,0.00001008449,0.0001424063,0.0001897,0.0001360055],"category_scores_gemma":[0.0001107778,0.0001040285,0.0001286099,0.0001099959,0.0004281932,0.0001632999,0.00005410478,0.0003263479,0.00008260823],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003114687,"about_ca_system_score_gemma":0.00008229694,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006276139,"about_ca_topic_score_gemma":0.000004918363,"domain_scores_codex":[0.9984884,0.0004544783,0.0005585526,0.000150477,0.00006141932,0.0002867117],"domain_scores_gemma":[0.9989263,0.0001503078,0.0004509129,0.0001173985,0.000308635,0.00004642225],"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":[0.0002310946,0.00006844322,0.02862434,0.00001461117,0.0003011457,0.00002664025,0.0002602814,0.000003485308,0.9566433,0.00001194427,0.000519876,0.01329488],"study_design_scores_gemma":[0.004598383,0.001852334,0.05830625,0.00009358047,0.0001362961,0.006187722,0.0003521566,0.00003132919,0.9254213,0.0007179664,0.00200671,0.000295997],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9914852,0.006509185,0.0008875671,0.0002758873,0.0001684563,0.0002149099,0.0004050694,0.000006910438,0.00004682873],"genre_scores_gemma":[0.9959626,0.002282321,0.0002845022,0.00007211412,0.00002457969,0.000003543709,0.00134193,0.000008193098,0.00002019387],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03122199,"threshold_uncertainty_score":0.424216,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02410645144481809,"score_gpt":0.2901929490526841,"score_spread":0.266086497607866,"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."}}