{"id":"W2996664506","doi":"10.1101/2019.12.19.883355","title":"Protein Docking and Steered Molecular Dynamics Reveal Alternative Regulatory Sites on the SERCA Calcium Transporter","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Ion channel regulation and function","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"Loyola University Chicago; National Institutes of Health; National Science Foundation","keywords":"SERCA; Phospholamban; Docking (animal); Chemistry; Biophysics; Calcium ATPase; Biochemistry; ATPase; Macromolecular docking; Cell biology; Transmembrane domain; Binding site; Calcium-binding protein; Calcium; Protein structure; Biology; Endoplasmic reticulum; Enzyme; Amino acid","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":[0.0002332168,0.0003995419,0.0005466273,0.0002687763,0.0005098967,0.0007264796,0.0006114935,0.0004239452,0.001761614],"category_scores_gemma":[0.000485512,0.0003162448,0.0004265525,0.000223903,0.0005716569,0.0004652129,0.0005082369,0.0005230475,0.000180345],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008429741,"about_ca_system_score_gemma":0.0007165154,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.006998965,"about_ca_topic_score_gemma":0.005434984,"domain_scores_codex":[0.9999013,0.00002598219,0.00000364501,0.00001832645,0.00002465915,0.00002600658],"domain_scores_gemma":[0.9998358,0.0000422718,0.00003211171,0.00001618812,0.00001835999,0.00005521022],"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":[0.0009162161,0.0002733773,0.006602955,0.0001097754,0.0001528943,0.0006435942,0.0002934824,0.8904921,0.08555277,0.008485882,0.0006795545,0.005797471],"study_design_scores_gemma":[0.00008844632,0.00008522022,0.001446554,0.000004416479,0.00001237418,0.00002396505,0.00005406749,0.9928616,0.004476991,0.0007547286,0.0001762115,0.00001547601],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9925818,0.00004698906,0.006129146,0.00008222985,0.000008628811,0.000008060774,0.00004402031,0.000098463,0.001000733],"genre_scores_gemma":[0.9977198,0.0000534267,0.001939839,0.00001603535,0.0000016373,0.00001015825,0.00005219251,0.00002009558,0.0001867222],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.006998965,"threshold_uncertainty_score":0.01391643,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01417839563148227,"score_gpt":0.2171647944006472,"score_spread":0.202986398769165,"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."}}