Computational Drug Discovery and Design
group matching information for an assayed molecule with the reference molecule DKPES (seeNote 2). Please note that this protocol ...
(within 1.3 A ̊) with the same group in DKPES. This functional group matching data is stored as a binary variable, where 0 indic ...
two sublots,ax[0]andax[1], showing a histogram of the signal inhibition and a scatter plot of the signal inhibition versus molec ...
Looking at the heat maps in Fig.9, the following conclusions can be drawn: l The top nine most active molecules have a sulfur ma ...
shows a signal inhibition of 60%. It matches the three terminal sulfate-oxygens and sulfur atom. However, a compound with the sa ...
impure—such a result would indicate that it was not a useful criterion for distinguishing between active and non-active mole- cu ...
Fig. 11Binary classification tree separating active from non-active compounds. After importing the tree submodule from the sciki ...
We conclude from the binary classification tree (Fig.11) that a majority of the active inhibitors (8 of 12) share a sulfur atom ...
Fig. 12Similar to fitting a DecisionTreeClassifier (Fig.11), we first initialize a newRandomForest- Classifierobject from scikit ...
3.5 Sequential Feature Selection with Logistic Regression As an alternative approach and to probe the robustness of our conclusi ...
that it is easy to interpret as a generalized linear model: The output always depends on the sum of the inputs and model paramet ...
The logistic regression implementation used in this section learns the weights for the parameters (matched chemical features) of ...
Fig. 14Performing sequential feature selection using logistic regression to identify features that discriminate between active a ...
group matching features) given a fixed number of samples in the training set, which will more likely result in overfitting and l ...
3.6 Conclusion From the decision tree analysis (section3.3), random forest feature importance estimation (section3.4), and seque ...
that do not appear substantially more frequently in active molecules than in non-actives (are not discriminatory of activity), f ...
Throughout section3, we assumed that the data frame of activity data was already sorted by signal inhibition in decreas- ing or ...
We chose a 1.3 A ̊ cutoff between overlayed atoms to identify functional group matches in 3D. If two molecules share the same a ...
overfitting problem in parametric regression, where including more terms with adjustable weights allows better fit to a set of t ...
recommended to exclude highly correlated features from the dataset for feature importance analysis, for instance, via recur- siv ...
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