{"id":"W2159972733","doi":"10.1085/jgp.201311049","title":"A computational study of barium blockades in the KcsA potassium channel based on multi-ion potential of mean force calculations and free energy perturbation","year":2013,"lang":"en","type":"article","venue":"The Journal of General Physiology","topic":"Ion channel regulation and function","field":"Biochemistry, Genetics and Molecular Biology","cited_by":21,"is_retracted":false,"has_abstract":true,"ca_institutions":"Memorial University of Newfoundland","funders":"National Institute of General Medical Sciences","keywords":"KcsA potassium channel; Chemistry; Ion; Molecular dynamics; Potential of mean force; Barium; Crystallography; Potassium channel; Binding site; Ion channel; Biophysics; Computational chemistry; Inorganic chemistry","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":[0.0002427561,0.00008310279,0.000136199,0.00008539355,0.00006258486,0.000005012788,0.0001403569,0.00006608575,0.000007992346],"category_scores_gemma":[0.00004051299,0.00004851495,0.00005530889,0.00007821783,0.00007178568,0.00000775215,0.00003137848,0.00007357531,1.579606e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00000793885,"about_ca_system_score_gemma":0.0000301487,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001040343,"about_ca_topic_score_gemma":0.00003374782,"domain_scores_codex":[0.9990383,0.0003417582,0.0003041509,0.00008526709,0.0001493363,0.00008123226],"domain_scores_gemma":[0.9992536,0.0000460326,0.0002812805,0.0001398234,0.0002585644,0.00002067004],"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":[0.0003047513,0.000298858,0.0000852925,0.000004709552,0.00003100538,1.749207e-7,0.0003481867,0.5563655,0.4420165,0.0001104274,0.0003112486,0.0001233018],"study_design_scores_gemma":[0.00350348,0.003185623,0.2102813,0.00001395683,0.00005937132,0.0000241985,0.001518714,0.7604069,0.01839024,0.002473277,0.00002696371,0.0001160658],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9878899,0.00004992969,0.01117726,0.0005845429,0.0001403799,0.000137672,0.000004602146,9.71503e-7,0.00001478803],"genre_scores_gemma":[0.9992372,0.00001144702,0.000158694,0.000221166,0.0002670475,0.000005280916,0.00003080665,0.000005843743,0.00006250079],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4236263,"threshold_uncertainty_score":0.1978382,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01175056687537167,"score_gpt":0.2333327694490704,"score_spread":0.2215822025736988,"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."}}