{"id":"W2143598945","doi":"10.1021/ct900460m","title":"Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber","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":262,"is_retracted":false,"has_abstract":true,"ca_institutions":"National Institute for Nanotechnology","funders":"National Institute of General Medical Sciences","keywords":"Solvation; Molecular dynamics; Dipeptide; Biomolecule; Computational chemistry; Molecular model; Chemistry; Chemical physics; Molecule; Materials science; Nanotechnology; Stereochemistry; 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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0005057652,0.00009796728,0.0001556378,0.00005015643,0.00001267559,0.000008325938,0.00007395337,0.0001300709,0.000003606851],"category_scores_gemma":[0.00009590957,0.0000772604,0.00005120968,0.00007136107,0.0001210978,0.000009004228,0.00003087699,0.000200675,9.72294e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001275815,"about_ca_system_score_gemma":0.00007383818,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001233063,"about_ca_topic_score_gemma":0.000005014756,"domain_scores_codex":[0.9993327,0.00005552626,0.0002638311,0.000112154,0.000148757,0.00008698368],"domain_scores_gemma":[0.9994084,0.00005530729,0.000236143,0.00008226839,0.0001734097,0.00004443136],"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":[0.001151431,0.00004567941,0.0004253308,0.00001526865,0.00004623798,0.00001148402,0.00002031262,0.00201361,0.9479914,0.04426152,0.000001553796,0.00401612],"study_design_scores_gemma":[0.001560115,0.0003397156,0.0008339974,0.00004950327,0.00005192756,0.0002312128,0.00003857262,0.01952635,0.6142926,0.3628933,0.00000778235,0.000174896],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7590787,0.0001321644,0.2405932,0.00003103841,0.00003560364,0.00005650346,0.00000176314,0.00000141823,0.00006961789],"genre_scores_gemma":[0.9925221,0.00000314978,0.007293955,0.00009922229,0.00003798889,0.0000012843,0.00002950193,0.0000103467,0.000002415914],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3336988,"threshold_uncertainty_score":0.3150588,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002835656445151447,"score_gpt":0.2207100557282315,"score_spread":0.2178743992830801,"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."}}