{"id":"W2978025815","doi":"10.1016/j.pbiomolbio.2019.09.003","title":"SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange","year":2019,"lang":"en","type":"review","venue":"Progress in Biophysics and Molecular Biology","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Calgary","funders":"National Institute of General Medical Sciences; National Institutes of Health; National Cancer Institute; National Institute on Aging; Natural Sciences and Engineering Research Council of Canada; Wellcome Trust","keywords":"Threading (protein sequence); Sequence (biology); Autophosphorylation; Computer science; Chemistry; Computational biology; Crystallography; Bioinformatics; Protein structure; Biology; Phosphorylation; Biochemistry; Protein kinase A","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000182324,0.0004772361,0.0009075922,0.00006074597,0.00004688722,0.00003790304,0.0008471961,0.0006962654,0.000001138132],"category_scores_gemma":[0.00004831273,0.0003166353,0.0001656302,0.0001543898,0.0007202742,0.000006331242,0.001245783,0.0003546787,6.728764e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002179573,"about_ca_system_score_gemma":0.0001595651,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002052702,"about_ca_topic_score_gemma":0.00000788587,"domain_scores_codex":[0.9979738,0.0002048329,0.0004013407,0.001002146,0.0001103585,0.0003075293],"domain_scores_gemma":[0.9982781,0.00005767939,0.0003837349,0.001172454,0.00005370389,0.00005425678],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001679238,0.0001418502,0.002595137,0.005342158,0.0005259046,0.00002516686,0.00007087603,0.000005740314,0.08828674,0.002210771,0.00000789519,0.9006199],"study_design_scores_gemma":[0.006899277,0.003822955,0.0003254332,0.04282419,0.003700993,0.000217286,0.00007306221,0.01156295,0.440083,0.02823865,0.4539351,0.008317052],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0391559,0.957544,0.0007700263,0.00002431427,0.000161288,0.0008304637,0.001458996,0.00000730362,0.000047664],"genre_scores_gemma":[0.1089008,0.881409,0.002557721,0.0002107867,0.0002196008,0.000134576,0.006472554,0.00008775516,0.000007178006],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.8923028,"threshold_uncertainty_score":0.9999286,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04407843765342167,"score_gpt":0.3722409485513921,"score_spread":0.3281625108979704,"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."}}