{"id":"W4407207002","doi":"10.1101/2025.02.03.636246","title":"P3a site-specific and cassette mutagenesis for seamless protein, RNA and plasmid engineering","year":2025,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Protein purification and stability","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill University Health Centre","funders":"Canadian Institutes of Health Research","keywords":"Mutagenesis; Plasmid; Protein engineering; P3a; Site-directed mutagenesis; Computational biology; Computer science; Biology; Genetics; Mutation; DNA; Gene; Biochemistry; Mutant","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001929569,0.001635572,0.001317135,0.001410028,0.0006551079,0.0008855871,0.001321433,0.001238868,0.003685296],"category_scores_gemma":[0.00128164,0.001112042,0.001369094,0.001324347,0.000613576,0.0007558582,0.001204854,0.00306908,0.004814832],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0005171896,"about_ca_system_score_gemma":0.0007808011,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000474922,"about_ca_topic_score_gemma":0.0007695907,"domain_scores_codex":[0.9976807,0.0006650071,0.0002100724,0.0004249122,0.0008120814,0.0002073372],"domain_scores_gemma":[0.9993687,0.000171994,0.000108238,0.0001920991,0.0000994791,0.00005941579],"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":[0.000108282,0.00008246023,0.00009843799,0.0003665474,0.00003470903,0.000166647,0.00005732126,0.0004070965,0.9781272,0.001692149,0.001718133,0.0171409],"study_design_scores_gemma":[0.00002796213,0.0002305803,0.0004156116,0.00002930993,0.00004176701,0.0009180053,0.00001442473,0.003221961,0.9624483,0.0006470019,0.03196522,0.00003986945],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04421232,0.002930786,0.9401725,0.0002788831,0.0003340797,0.001268667,0.001965858,0.004368002,0.004468905],"genre_scores_gemma":[0.1750326,0.005523285,0.795489,0.000385473,0.00007862661,0.002790372,0.007051601,0.001932175,0.01171693],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003685296,"threshold_uncertainty_score":0.01232857,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009835344939876603,"score_gpt":0.2109256100747861,"score_spread":0.2010902651349095,"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."}}