{"id":"W2147803109","doi":"10.1093/bioinformatics/btv274","title":"SpeeDB: fast structural protein searches","year":2015,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"Carleton University","funders":"Natural Sciences and Engineering Research Council of Canada; National Research Foundation","keywords":"Protein Data Bank (RCSB PDB); Computer science; Protein Data Bank; Protein superfamily; Interface (matter); Computational biology; Function (biology); Protein structure; Identification (biology); Stability (learning theory); Data mining; Information retrieval; Chemistry; Biology; Machine learning; Stereochemistry; Biochemistry; Genetics","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":[0.0001458903,0.0001472212,0.0001113081,0.00003600102,0.00005446118,0.00005045371,0.0002240293,0.0001376548,0.000008201509],"category_scores_gemma":[0.00010257,0.0001204447,0.00005380459,0.00007874766,0.00008518203,0.00001160479,0.0001600778,0.00009442271,0.0000509021],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002065392,"about_ca_system_score_gemma":0.0001479275,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001067498,"about_ca_topic_score_gemma":0.00001221628,"domain_scores_codex":[0.9991854,0.00001810747,0.0002170527,0.0001141909,0.0002106672,0.0002545266],"domain_scores_gemma":[0.9993157,0.000002269504,0.00007851877,0.0003242056,0.0001112442,0.0001679942],"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":[0.001548939,0.0001767883,0.01691026,0.001146474,0.0007579317,0.00005397587,0.008250216,0.002691993,0.5527313,0.0237653,0.0641805,0.3277863],"study_design_scores_gemma":[0.006717972,0.003048256,0.004377646,0.0001260335,0.00008315024,0.0005389407,0.005453297,0.07896832,0.5458629,0.01383126,0.3380319,0.00296037],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.96877,0.0002316353,0.01233299,0.000154894,0.0002247617,0.0005152306,0.00007070449,0.00004980153,0.01764995],"genre_scores_gemma":[0.9454456,0.000007502671,0.0519919,0.00025955,0.0003146209,0.00001400634,0.0003027533,0.00002077619,0.001643264],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3248259,"threshold_uncertainty_score":0.4911591,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01925297353223119,"score_gpt":0.2571173499731011,"score_spread":0.2378643764408699,"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."}}