{"id":"W4392755399","doi":"10.1002/jcc.27318","title":"Resolving coupled pH titrations using alchemical free energy calculations","year":2024,"lang":"en","type":"article","venue":"Journal of Computational Chemistry","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":10,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"","keywords":"Protonation; Formalism (music); Chemistry; Statistical physics; Coupling constant; Titration; Molecular dynamics; Computational chemistry; Thermodynamics; Physics; Physical chemistry; Quantum mechanics","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":[0.00009893422,0.0001043773,0.0001127329,0.00003552443,0.00006986387,0.00005342425,0.0001690164,0.0001243229,0.00003808704],"category_scores_gemma":[0.00009822568,0.00009987393,0.0001445055,0.0001074543,0.00005151286,0.00001150819,0.00005466151,0.0001463114,5.851225e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004315561,"about_ca_system_score_gemma":0.0003866635,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004087417,"about_ca_topic_score_gemma":0.000001435445,"domain_scores_codex":[0.9991884,0.00001302116,0.0003222992,0.0001355485,0.0002300185,0.000110697],"domain_scores_gemma":[0.9994059,0.0000378808,0.000113118,0.0001241114,0.0002405555,0.00007843576],"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":[0.00002465886,0.00002109115,0.00004364319,0.00003261263,0.0001136898,0.00002190591,0.00001537058,0.1281404,0.8692745,0.0004272077,0.001632421,0.0002524519],"study_design_scores_gemma":[0.001211636,0.0001115134,0.0003363654,0.0002608392,0.000208431,0.002954959,0.00006238555,0.4454238,0.4486666,0.06914171,0.03104275,0.0005789982],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7071661,0.002549387,0.2888277,0.0003225328,0.0002001907,0.00002954129,0.00003349455,0.00001308892,0.0008579817],"genre_scores_gemma":[0.9794382,0.0000226229,0.01919188,0.00009008477,0.0009332698,0.000001172837,0.0001191368,0.00001706537,0.0001865019],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4206079,"threshold_uncertainty_score":0.407274,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00840801487461618,"score_gpt":0.2627321898482922,"score_spread":0.254324174973676,"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."}}