{"id":"W2030488214","doi":"10.1021/ct9006597","title":"Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations","year":2010,"lang":"en","type":"article","venue":"Journal of Chemical Theory and Computation","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":27,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hospital for Sick Children; University of Toronto; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Serotonin transporter; Free energy perturbation; Molecular dynamics; Transporter; Chemistry; Serotonin Plasma Membrane Transport Proteins; Biophysics; Computational chemistry; Biochemistry; Serotonin; Receptor; Biology","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":[0.0002380239,0.00006680975,0.00009492796,0.00002197344,0.00007617251,0.00001261723,0.0001312995,0.00006164479,0.000001223718],"category_scores_gemma":[0.0001483134,0.00003615149,0.00004659241,0.00004891206,0.0001085107,0.00001194094,0.00003643531,0.00008706346,9.025669e-9],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000002397398,"about_ca_system_score_gemma":0.00002919933,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001197674,"about_ca_topic_score_gemma":0.00001261731,"domain_scores_codex":[0.9995406,0.00004457668,0.0001755364,0.0000815287,0.00009769011,0.00006009451],"domain_scores_gemma":[0.9994199,0.0001209415,0.0001617668,0.0001256658,0.0001422885,0.00002939665],"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":[0.0002957297,0.00001102424,0.000107421,0.000008143045,0.00006766742,1.622134e-7,0.0002020945,0.004541538,0.9843028,0.00815139,0.00002628438,0.002285799],"study_design_scores_gemma":[0.0009552825,0.0001755095,0.001976293,0.00003178652,0.0001323271,0.00004324083,0.00006462051,0.002467179,0.9267907,0.06697682,0.0003016792,0.00008454435],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8790366,0.0001176403,0.1203077,0.000337444,0.00004963637,0.00008574907,0.00003331687,0.000001134624,0.000030724],"genre_scores_gemma":[0.9962357,0.00001212231,0.003532366,0.00008811003,0.00009526807,0.000003329561,0.00001145339,0.000005860663,0.00001584222],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.117199,"threshold_uncertainty_score":0.1474215,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006893266221967968,"score_gpt":0.2535556181667333,"score_spread":0.2466623519447654,"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."}}