3D QSAR Models

v1.2.0 August 2025

General Notice

  • This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.0, and OpenEye-Snowball==0.30.0.

Floe Updates

  • 3D QSAR Model: Builder

    • The floe now allows users to select a set of 3D models to build.

    • Two new 3D models, ROCS-GPR-NO-2D and EON-GPR-NO-2D, have been added. Unlike ROCS-GPR and EON-GPR, these two GPR models only use 3D Tanimoto as descriptors.

    • The floe now accepts kcal/mol and kJ/mol as potency units.

    • The default cross-validation method has been switched from “leave one out” to “random” to accommodate for a larger training set.

    • The option Include 2D in COMBO has been added to allow the user to decide whether to incorporate 2D-GPR into final model predictions.

    • A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.

  • 3D QSAR Model: Interpretation

    • Grids corresponding to color atom probes have been added to the output dataset, along with contour values used for generating high and low surfaces.

    • The domain grid has been deleted from the output dataset.

    • The Generate ROCS Query parameter has been removed. ROCS query output will be generated by default along with ROCS-kPLS model interpretation.

    • A new parameter, Selected Models, has been added, allowing for the selection of kPLS models to interpret.

    • A new parameter, Percentage for Surface Contour Values, has been added to give the user more flexibility to choose contour values for high and low surfaces.

    • A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.

  • 3D QSAR Model: Validation

    • A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.

  • 3D QSAR Model: Predictor

    • A new parameter section, Cube Memory Parameters, has been added to allow users to increase the memory of some cubes for relatively large training sets to avoid cube memory errors.