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In this study, the pentachlorothiophenol (PCTP) and Chinese rare minnow (Gobiocypris rarus) transthyretin were selected as the objects of study. We determined the potential binding affinity data of pentachlorothiophenol on Chinese rare minnow transthyretin, revealed the underlying molecular recognition mechanism between pentachlorothiophenol and the protein, and derived the binary classification models for distinguishing whether a given substance was a potential Chinese rare minnow transthyretin disruptor or not by using the Chinese rare minnow transthyretin disrupting data measured in this study and previous studies. The experimental results indicated that the observed water solubility value of pentachlorothiophenol was (0.636 ± 0.0871) mg/L (25℃). The relative competing potency of pentachlorothiophenol with 3,3′,5,5′-Tetraiodo-L-thyronine (T4) binding to Chinese rare minnow transthyretin (logRP) was (0.0200 ± 0.0533), implying that pentachlorothiophenol was a high potency Chinese rare minnow transthyretin disruptor. The molecular simulation results documented that the binding interaction between pentachlorothiophenol and Chinese rare minnow transthyretin was controlled by the halogen hydrogen bond, halogen bond, and hydrophobic interactions. In the modelling, three optimum binary classification models (i.e. k nearest neighbour model, random forest model, decision tree model) were successfully developed. The statistical parameters (e.g. predictive accuracy (Q)) values of those optimum models were 1, highlighting that those optimum models had great classification performance. Finally, the tool named "TTR Profiler" that used to identify potential transthyretin disruptors was updated by integrating the newly developed optimum models, which means that the application domain of the related models in the new tool covered the thiophenols.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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