{"id":"W1895661004","doi":"10.1021/acs.biochem.5b00753","title":"Conformational Changes of the Antibacterial Peptide ATP Binding Cassette Transporter McjD Revealed by Molecular Dynamics Simulations","year":2015,"lang":"en","type":"article","venue":"Biochemistry","topic":"Drug Transport and Resistance Mechanisms","field":"Medicine","cited_by":25,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Calgary","funders":"Canadian Institutes of Health Research; Alberta Innovates - Health Solutions","keywords":"Transporter; Transmembrane domain; Molecular dynamics; ATP-binding cassette transporter; Peptide; Biophysics; ATP hydrolysis; Transmembrane protein; Ligand (biochemistry); Chemistry; Transport protein; Protein structure; Crystallography; Stereochemistry; Membrane; Biochemistry; Biology; ATPase; Enzyme; Receptor; Computational chemistry","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":[0.00008857912,0.0001189473,0.0001799274,0.0000221834,0.00004215361,0.000007509992,0.0001016523,0.0001189938,0.00004712649],"category_scores_gemma":[0.00001425812,0.00008875765,0.00008508765,0.0001122983,0.00007328576,0.00003040869,0.000008913678,0.00009889629,0.000002147053],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000805876,"about_ca_system_score_gemma":0.0001867209,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000006515793,"about_ca_topic_score_gemma":0.000009093352,"domain_scores_codex":[0.9991913,0.000007079524,0.0002264462,0.000129943,0.000296823,0.0001483675],"domain_scores_gemma":[0.999438,0.000008835345,0.0001158785,0.0002282812,0.0001102079,0.00009874785],"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":[0.00008469667,0.00005059717,0.004416699,0.0001676301,0.00004641589,0.000008713847,0.0002440368,0.00001191671,0.9941745,0.0000487461,0.0007009034,0.00004507599],"study_design_scores_gemma":[0.001480794,0.0000298876,0.002026972,0.0001861496,0.0001391292,0.00002071779,0.0002588628,0.0006002334,0.9925187,0.00002389722,0.002563216,0.0001514043],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9957934,0.00006116057,0.0006076353,0.001567801,0.0001610559,0.0001718558,0.0006278835,0.00002344511,0.0009857374],"genre_scores_gemma":[0.996243,0.000004868879,0.0003037949,0.0001535917,0.00007789792,0.000004151771,0.001231124,0.0000147126,0.001966854],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.002389727,"threshold_uncertainty_score":0.3619432,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01139895625768056,"score_gpt":0.237699773135361,"score_spread":0.2263008168776804,"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."}}