{"id":"W1964009616","doi":"10.1021/ct200390j","title":"Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations","year":2012,"lang":"en","type":"article","venue":"Journal of Chemical Theory and Computation","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":24,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Medical Research Council; Eidgenössische Technische Hochschule Zürich","keywords":"Solvation; Molecular dynamics; Force field (fiction); Implicit solvation; Atom (system on chip); Solvent; Chemistry; Water model; Accessible surface area; Solvent models; Computational chemistry; Statistical physics; Representation (politics); Molecule; Chemical physics; Thermodynamics; Physics; Computer science; Organic 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":[0.000233313,0.00008760076,0.0001250722,0.00004008626,0.00002495476,0.00001655913,0.00005879682,0.0001109324,0.00000408771],"category_scores_gemma":[0.00004239891,0.00006886037,0.0000539,0.000036899,0.00002370087,0.00002236609,0.00003770072,0.00009693883,3.604268e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002301437,"about_ca_system_score_gemma":0.00001158741,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001588907,"about_ca_topic_score_gemma":0.000001816377,"domain_scores_codex":[0.999357,0.00007226456,0.0002504308,0.00009074892,0.00008095162,0.0001486066],"domain_scores_gemma":[0.9996657,0.00004744962,0.0001106832,0.00006123525,0.00005574676,0.00005922636],"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":[0.0002127361,0.00004050507,0.00253761,0.000005655798,0.00003193356,8.403698e-7,0.0004186586,0.003558968,0.9902269,0.000877356,0.000001986829,0.002086816],"study_design_scores_gemma":[0.0009133453,0.00008140825,0.002416215,0.00002012327,0.00003961283,0.00002175595,0.0002542417,0.01425167,0.9047153,0.077102,0.0000255358,0.0001587685],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7454228,0.0001598607,0.2542564,0.00003607467,0.00004479437,0.00004967211,0.000008018044,0.000001739884,0.00002061998],"genre_scores_gemma":[0.9950778,0.000008937145,0.004353562,0.0001735911,0.0000909432,0.000001701934,0.0002830348,0.000008401524,0.000002019489],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2499028,"threshold_uncertainty_score":0.2808044,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005386778874484539,"score_gpt":0.2472369367732152,"score_spread":0.2418501578987307,"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."}}