{"id":"W2595859407","doi":"10.1039/c7cp01028a","title":"Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels","year":2017,"lang":"en","type":"article","venue":"Physical Chemistry Chemical Physics","topic":"DNA and Nucleic Acid Chemistry","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Molecular dynamics; G-quadruplex; Umbrella sampling; DNA; Ion channel; Sampling (signal processing); Chemistry; Ion; Biophysics; Chemical physics; Computational biology; Nanotechnology; Computational chemistry; Physics; Biology; Materials science; Biochemistry","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.00005554829,0.000539583,0.0004683044,0.000004923797,0.0003765146,0.000164629,0.0009637828,0.0003462672,0.00002713132],"category_scores_gemma":[0.0001901692,0.0005852844,0.0003908338,0.00008044476,0.0004749913,0.00003087946,0.0006435809,0.0004119881,0.00001815084],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001501151,"about_ca_system_score_gemma":0.0001159486,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000198108,"about_ca_topic_score_gemma":3.256801e-7,"domain_scores_codex":[0.9975703,0.0000171585,0.0003765036,0.0009627971,0.0004256468,0.0006476287],"domain_scores_gemma":[0.997583,0.00003774876,0.000357317,0.001568278,0.0001929282,0.0002607638],"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":[0.00006893212,0.0003826884,0.00005909378,0.0001341517,0.0001328884,0.000005442294,0.0000570973,0.000827672,0.9969679,0.0002896093,0.0003805698,0.0006939882],"study_design_scores_gemma":[0.0009107572,0.00003318303,0.00001573438,0.00005560563,0.00007992225,0.00000362064,0.00003198961,0.008847266,0.9791732,0.009093503,0.001080541,0.0006746656],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9870605,0.00005389529,0.004273742,0.0003248507,0.0001163215,0.0001875423,0.0002013227,0.00006754496,0.007714257],"genre_scores_gemma":[0.994517,0.00001322676,0.0005222186,0.0003278931,0.002346387,0.00003213057,0.00151338,0.00009567238,0.0006320851],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01779465,"threshold_uncertainty_score":0.9996598,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02450460934455938,"score_gpt":0.3013780873915269,"score_spread":0.2768734780469675,"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."}}