{"id":"W1998431713","doi":"10.1021/bi0513498","title":"Strongly Hydrogen-Bonded Water Molecule Present near the Retinal Chromophore of <i>Leptosphaeria</i> Rhodopsin, the Bacteriorhodopsin-like Proton Pump from a Eukaryote","year":2005,"lang":"en","type":"article","venue":"Biochemistry","topic":"Photoreceptor and optogenetics research","field":"Neuroscience","cited_by":40,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"","keywords":"Bacteriorhodopsin; Photoisomerization; Rhodopsin; Molecule; Hydrogen bond; Proton; Chemistry; Retinal; Photochemistry; Halorhodopsin; Photoprotein; Chromophore; Halobacteriaceae; Neurospora; Crystallography; Halobacterium salinarum; Mutant; Isomerization; Biochemistry; Membrane; Organic chemistry; Physics","routes":{"ca_aff":true,"ca_fund":false,"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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.0003416222,0.0003277561,0.0002643398,0.00001998123,0.000465409,0.0002420456,0.001448445,0.0001724523,0.001100185],"category_scores_gemma":[0.000129563,0.0001817832,0.0002004621,0.0002294607,0.00104792,0.00007737117,0.0005695372,0.0004604771,0.00009420134],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000822752,"about_ca_system_score_gemma":0.0002352164,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000152591,"about_ca_topic_score_gemma":0.000003919261,"domain_scores_codex":[0.9970138,0.000237535,0.0004431655,0.0007015133,0.0008970795,0.0007069038],"domain_scores_gemma":[0.9982782,0.0001526536,0.0001505867,0.001125179,0.0001066109,0.0001867552],"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":[0.0002115278,0.0001423628,0.0003907813,0.0000427729,0.00002307399,0.000008936512,0.000541287,0.00004526273,0.9971104,0.000001538688,0.001078643,0.0004033714],"study_design_scores_gemma":[0.0005032704,0.00006556031,0.0002152304,0.00003628963,0.00002112534,0.00001912816,0.00006804522,0.001739137,0.9757857,0.00001986188,0.02129686,0.0002297447],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9951894,0.0003961931,0.000007970929,0.001927728,0.0001304723,0.0009647619,0.0002050833,0.00004728112,0.001131155],"genre_scores_gemma":[0.9974611,0.0001145484,0.0001291925,0.0003053776,0.000453865,0.0002756977,0.00003945282,0.00005075815,0.001169993],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0213247,"threshold_uncertainty_score":0.999813,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02062037726537829,"score_gpt":0.2672809685443258,"score_spread":0.2466605912789475,"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."}}