{"id":"W2968294177","doi":"10.3390/molecules24162908","title":"Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations","year":2019,"lang":"en","type":"article","venue":"Molecules","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":15,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph; University of Lethbridge","funders":"Natural Sciences and Engineering Research Council of Canada; Western Canada Research Grid; Compute Canada; University of Lethbridge","keywords":"Aptamer; Nucleoside; Nucleobase; Deoxyuridine; DNA; Chemistry; Thrombin; Combinatorial chemistry; Computational biology; Biochemistry; Biology; Molecular biology","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":[],"consensus_categories":[],"category_scores_codex":[0.00007262512,0.0002264394,0.0002129923,0.00001899317,0.0001286563,0.00002282566,0.0006131308,0.0001705256,0.00007866757],"category_scores_gemma":[0.0001628441,0.0001173714,0.0003170139,0.0001384535,0.0003127967,0.000006599258,0.0002530774,0.0001749151,0.00000376296],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003815734,"about_ca_system_score_gemma":0.00008749515,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001537613,"about_ca_topic_score_gemma":0.00001363131,"domain_scores_codex":[0.9987551,0.0001833638,0.0003035921,0.0003056776,0.0002737239,0.0001785348],"domain_scores_gemma":[0.9985098,0.00007398632,0.0002631864,0.0009983268,0.0001109334,0.00004381359],"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":[0.0005928734,0.00005596219,0.0004407903,0.000009298383,0.0001206309,3.200811e-7,0.0001645722,0.0006955549,0.9973643,0.000217266,0.000258136,0.00008029759],"study_design_scores_gemma":[0.0004865997,0.0001545266,0.03935191,0.00005153013,0.00003194817,0.000001918763,0.00005517436,0.0009024472,0.9574632,0.001245884,0.0001088316,0.0001460066],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9982528,0.0001158184,0.00003059481,0.0006158303,0.00005868279,0.0003854255,0.0001209574,0.000008473537,0.000411392],"genre_scores_gemma":[0.9993921,0.000006483032,0.00009334202,0.0002228759,0.00005034762,0.00000761889,0.00008780601,0.00002893202,0.0001104883],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03990107,"threshold_uncertainty_score":0.4786267,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007769922527960838,"score_gpt":0.2391576137875002,"score_spread":0.2313876912595393,"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."}}