{"id":"W1979860914","doi":"10.1021/jp304760k","title":"Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G<sub>3</sub>T<sub>4</sub>G<sub>4</sub>)]<sub>2</sub> G-Quadruplex DNA Structure","year":2012,"lang":"en","type":"article","venue":"The Journal of Physical Chemistry B","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"","keywords":"Ion; Molecular dynamics; Stacking; Chemistry; G-quadruplex; Crystallography; Chemical physics; Molecular physics; Computational chemistry; DNA","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002611022,0.0006704329,0.0008563212,0.0002891631,0.0006218484,0.0004963322,0.001012879,0.00107685,0.003374639],"category_scores_gemma":[0.00095216,0.0003079805,0.0005983628,0.0004803799,0.0003903277,0.0007331861,0.0003687865,0.001239691,0.0003470375],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009914823,"about_ca_system_score_gemma":0.001206201,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01081499,"about_ca_topic_score_gemma":0.01140175,"domain_scores_codex":[0.9998882,0.00001950886,0.000004960936,0.00002350934,0.00003396657,0.000029798],"domain_scores_gemma":[0.9995815,0.0001796116,0.00004724003,0.00002732526,0.000104144,0.00006022854],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0003067041,0.0003236177,0.00426095,0.0002294705,0.0001993775,0.000270476,0.0001995402,0.9529555,0.02440711,0.008691785,0.001502733,0.006652732],"study_design_scores_gemma":[0.0000735917,0.00006632377,0.0006328803,0.000007160372,0.00002189006,0.00002136924,0.00003291024,0.9942271,0.002930196,0.0008035389,0.001171935,0.00001108664],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9654987,0.0005053036,0.02416675,0.0004520376,0.0001026682,0.00009823635,0.001169202,0.000349764,0.007657359],"genre_scores_gemma":[0.9586836,0.0004506895,0.03712373,0.0002150371,0.00002464797,0.0003469859,0.001438111,0.000122723,0.001594474],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01081499,"threshold_uncertainty_score":0.0215041,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005105490203335184,"score_gpt":0.2193715285978936,"score_spread":0.2142660383945585,"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."}}