Build Atom-Based Model Dialog Box

Build Atom-Based Model Dialog Box Features

• Grid spacing text box
• Maximum PLS factors text box
• Eliminate variables with |t-value| < option and text box
• Number of ligands to leave out text box

Grid spacing text box

Length of the sides of the cubic volume elements, which are arranged in a 3D grid covering the space occupied by the ligands. Valid range is 0.5 Å to 2.0 Å.

Maximum PLS Factors text box

Maximum number of partial least squares factors in the regression model. You can choose any value, but you should not generally set this value to more than N/5, where N is the number of ligands in the training set, because of the risk of overfitting. To avoid overfitting, the standard deviation of regression should be larger than the experimental uncertainty in the activity values for the model that you use.

Eliminate variables with |t-value| < option and text box

Select this option to use a t-value filter to eliminate independent variables (i.e. bits) whose regression coefficients are overly sensitive to small changes in the training set composition, and enter the threshold for eliminating variables in the text box. The resulting models have fewer uninformative variables and tend to give better predictions on test set compounds.

Number of ligands to leave out text box

Set the number of ligands to be used in the leave-N-out cross-validation statistics. The default is 1.