{"id":"W2170533290","doi":"10.1016/j.jmb.2003.10.071","title":"Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues","year":2003,"lang":"en","type":"article","venue":"Journal of Molecular Biology","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":54,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Alberta","funders":"","keywords":"Phosphodiester bond; Stacking; Protein Data Bank (RCSB PDB); DNA; Hydrogen bond; Chemistry; Sequence (biology); Base pair; Nucleotide; Crystallography; Purine; Stereochemistry; Biochemistry; Molecule; Enzyme; Gene; RNA","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":[0.0002506775,0.0001548122,0.0002550682,0.00006796612,0.00004523169,0.00001052434,0.0001781539,0.000159477,0.00004839763],"category_scores_gemma":[0.0001834982,0.0001255204,0.0001255596,0.0000973261,0.0001666631,0.000008947923,0.00002718531,0.0001676736,0.000001642146],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002175625,"about_ca_system_score_gemma":0.0001148885,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006146239,"about_ca_topic_score_gemma":0.000005273977,"domain_scores_codex":[0.9989733,0.0001135206,0.0004035475,0.000193296,0.000116761,0.0001995832],"domain_scores_gemma":[0.9989447,0.00001812478,0.0005278612,0.0001712952,0.0002531226,0.00008491077],"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":[0.0001507967,0.00007092952,0.001928515,0.00001494986,0.0002082347,0.00002070187,0.00002388638,0.000008237157,0.9965739,0.00006029941,0.0005489031,0.0003906932],"study_design_scores_gemma":[0.0006039168,0.0007913089,0.00003365529,0.00004716399,0.00006929984,0.0004869952,0.0001718979,0.000002698782,0.9887912,0.000381372,0.008473083,0.0001473817],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9917642,0.001782115,0.005176724,0.0001163416,0.00009890425,0.00005645248,0.00002379596,0.000003810179,0.0009776221],"genre_scores_gemma":[0.9960084,0.000204049,0.003383344,0.0001280777,0.00006317339,0.00000300275,0.00007518309,0.000018697,0.0001160542],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.00792418,"threshold_uncertainty_score":0.5118573,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01000016845861541,"score_gpt":0.2637972752528133,"score_spread":0.2537971067941979,"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."}}