{"id":"W4205981810","doi":"10.26434/chemrxiv.13663544","title":"SBMOpenMM: A Builder of Structure-Based Models for OpenMM","year":2021,"lang":"en","type":"preprint","venue":"ChemRxiv","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Generalitat de Catalunya; European Commission; University of Victoria","keywords":"Python (programming language); Computer science; Programming language; Computational biology; R package; Folding (DSP implementation); Operating system; Biology; Engineering","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002529284,0.002774221,0.002693262,0.001785734,0.001956976,0.00288424,0.008458519,0.002649326,0.06766748],"category_scores_gemma":[0.006070593,0.002881103,0.003138286,0.001768501,0.001108866,0.003323581,0.005299198,0.006595137,0.03201909],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001572673,"about_ca_system_score_gemma":0.00433748,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005849323,"about_ca_topic_score_gemma":0.008050038,"domain_scores_codex":[0.9988681,0.0002131566,0.00008114174,0.0001855853,0.0005088547,0.0001432639],"domain_scores_gemma":[0.998454,0.0006325205,0.0001065186,0.0002977369,0.0003057924,0.000203459],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0007440967,0.0005352418,0.003618577,0.003364748,0.001188299,0.001226321,0.0009369486,0.1454301,0.01931769,0.09466603,0.6023246,0.1266474],"study_design_scores_gemma":[0.00039898,0.00007867524,0.0007251018,0.000275129,0.0001072893,0.0003442494,0.00008554325,0.6003186,0.01622355,0.0490517,0.3321846,0.0002066579],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.006283555,0.0006908365,0.6424021,0.0006460264,0.0005798376,0.0003478138,0.0232488,0.3108609,0.01494021],"genre_scores_gemma":[0.05117803,0.001474767,0.6456007,0.001038544,0.0002597427,0.002821429,0.05813491,0.2249976,0.01449423],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.06766748,"threshold_uncertainty_score":0.2263703,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0144200996073296,"score_gpt":0.2468475350784231,"score_spread":0.2324274354710935,"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."}}