{"id":"W2951264695","doi":"10.1371/journal.pcbi.1003569","title":"A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations","year":2014,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":110,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Sherbrooke","funders":"Canadian Institutes of Health Research","keywords":"Molecular dynamics; Dynamics (music); Statistical physics; Protein Interaction Networks; Protein structure prediction; Computer science; Physics; Materials science; Protein structure; Chemistry; Biology; Genetics; Protein–protein interaction; Computational chemistry","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":[0.0002511884,0.00007618864,0.0001479274,0.00002087581,0.00004729562,0.000004187475,0.00008610841,0.00008566026,2.450797e-7],"category_scores_gemma":[0.0003308089,0.00003983669,0.00003566056,0.00007693477,0.0001994625,0.000004439262,0.00004812162,0.00006357814,2.771741e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000004439829,"about_ca_system_score_gemma":0.00002380461,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001160796,"about_ca_topic_score_gemma":0.00003706342,"domain_scores_codex":[0.9991684,0.000361078,0.0002170229,0.0001153437,0.00006888658,0.00006928606],"domain_scores_gemma":[0.9990178,0.0006048167,0.0001765969,0.0001006257,0.00009085491,0.000009345553],"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":[0.0003333957,0.00001412239,0.01304546,0.00004273295,0.00004909006,3.37842e-8,0.00007952884,0.9337294,0.01481428,0.03762688,8.524346e-7,0.0002641931],"study_design_scores_gemma":[0.001067739,0.000311242,0.01550593,0.00002098455,0.00003586044,0.000002860035,0.000005798968,0.9709241,0.0008450142,0.01124535,0.000002649877,0.00003249979],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9358913,0.00008468991,0.06325104,0.00007831868,0.00001661301,0.0005796438,0.0000827182,0.000001826574,0.00001388912],"genre_scores_gemma":[0.9992203,0.000003944186,0.0005237013,0.00003668091,0.00002106011,0.00002863062,0.0001587017,0.000004439161,0.000002603255],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06332898,"threshold_uncertainty_score":0.1624493,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007134480059099461,"score_gpt":0.2240096909053057,"score_spread":0.2168752108462063,"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."}}