Machine learning and molecular simulation based methods for enhancing binding and activity prediction
A machine learning model and technology for simulating data, applied in the field of machine learning, can solve problems such as futility
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Embodiment 1
[0094] The following examples are provided to illustrate the claimed invention, but not to limit the claimed invention.
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Embodiment 2
[0101] A backbone split was defined where (1) agonist ligands with a Tanimoto score ≤0.5 compared to fentanyl were put into the training set, and (2) agonist ligands with a Tanimoto score ≥0.7 compared to fentanyl into the test set, and (3) antagonists are randomly distributed between the training and test sets.
[0102] a)
[0103] Fentanyl analog ligands (test set):
[0104] ['acetylfentanyl', 'propylenefentanyl', '3-allylfentanyl', 'alpha-methylthiofentanyl', 'aziridine', 'beta-hydroxyfentanyl' , 'β-hydroxythiofentanyl', 'butyrylfentanyl', 'carfentanyl', 'norprudin', 'dienprotine', 'fentanyl', '4-fluorobutyrylfentanyl' fentanyl', 'furylfentanyl', 'lofentanyl', '4-methoxybutyrylfentanyl', 'α-methylacetylfentanyl', '3-methylbutyrylfentanyl', 'n-methylcarbfentanyl', '3-methylfentanyl', 'β-methylfentanyl', '3-methylthiofentanyl', 'Ofentanyl', ' hydroxymethylfentanyl', 'p-flufentanyl', 'pepap', 'phenacramine', 'phenaridine', '4-phenylfentanyl', 'predidine', 'prodilidine' Ru...
Embodiment 3
[0119]The Random Forest average Gini impurity reduction ("importance") for each feature (MD state, crystal structure) was used to a) distinguish opioid agonists from antagonists, and b) distinguish opiates from μOR conjugates and nonconjugates.
[0120] a)
[0121] inactive crystals 0.063488 active crystal 0.01358 state 14 0.033463 state 12 0.013346 state 3 0.031175 state 6 0.012534 state 17 0.02995 state 2 0.012306 state 10 0.029853 state 1 0.012289 state 23 0.025154 state 20 0.01123 state 5 0.024361 state 16 0.023912 state 21 0.023884 state 4 0.021384 state 22 0.020618 state 0 0.019934 state 13 0.01972 state 18 0.017975 state 7 0.017955 state 24 0.017434 state 11 0.017295 state 9 0.01617 state 8 0.015486 state 15 0.015193 state 19 0.013673
[0122] b)
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