{"id":"W2006102249","doi":"10.1021/bi049158c","title":"FTIR Spectroscopy of the K Photointermediate of <i>Neurospora</i> Rhodopsin:  Structural Changes of the Retinal, Protein, and Water Molecules after Photoisomerization","year":2004,"lang":"en","type":"article","venue":"Biochemistry","topic":"Photoreceptor and optogenetics research","field":"Neuroscience","cited_by":51,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Guelph","funders":"University of Guelph","keywords":"Bacteriorhodopsin; Photoisomerization; Rhodopsin; Chemistry; Halorhodopsin; Halobacterium salinarum; Isomerization; Neurospora; Halobacteriaceae; Retinal; Photochemistry; Halobacterium; Photoprotein; Hydrogen bond; Molecule; Crystallography; Chromophore; Stereochemistry; Neurospora crassa; Membrane; Biochemistry; Organic chemistry","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":[0.00006730874,0.000125229,0.0001455811,0.00002154895,0.0000515,0.00001318892,0.0003827196,0.00006074928,0.00003800576],"category_scores_gemma":[0.0001203948,0.00006741078,0.00006748442,0.0001664449,0.0007259282,0.00002310257,0.0002377817,0.000120277,4.208102e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001833896,"about_ca_system_score_gemma":0.00005174781,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002060215,"about_ca_topic_score_gemma":0.000003041056,"domain_scores_codex":[0.998945,0.00004877994,0.0002012177,0.0002419564,0.0003685567,0.0001944863],"domain_scores_gemma":[0.9993613,0.00001474898,0.0001424579,0.0003816396,0.00006055518,0.00003925221],"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":[0.0001030816,0.00002400097,0.001305526,0.0001796733,0.000002533076,8.701929e-7,0.0002147026,0.000002206392,0.998143,0.000004680591,0.000004607035,0.00001513046],"study_design_scores_gemma":[0.0002781716,0.00006302797,0.002699633,0.00010185,0.000006371959,0.000007839225,0.00002371154,0.0000161171,0.9965785,0.0001353585,0.00001603753,0.00007335558],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.999097,0.00007608827,0.000002590397,0.0001718382,0.00008005226,0.000336733,0.00009758231,0.000005589665,0.0001325381],"genre_scores_gemma":[0.9996707,0.0000486779,0.00008042206,0.00006749383,0.00002446254,0.00002091759,0.000002155694,0.00001398971,0.00007111217],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001564463,"threshold_uncertainty_score":0.2748932,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009965312007333879,"score_gpt":0.2413703988453418,"score_spread":0.2314050868380079,"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."}}