Knowledge Base

I would like to construct a model for structure-activity relationships, and predict the activity of new compounds. How can I do this?

There are a number of ways in which you can construct a structure-activity or structure-property model with Schrödinger software. As activity is simply one kind of property, the methods can be applied to either QSAR or QSPR.

If you want to use 3D information for your model, you have the following options:

  • Atom-based QSAR — This method uses atom types and their occupancy of a grid of cubes as independent variables for fitting and predicting properties. In Maestro, choose

      TASKS → Browse  Discovery Informatics and QSAR → Atom-Based...

  • Field-based QSAR — This method is an implementation of the ComFA/ComSIA approach that uses the values of potentials on a grid for fitting and predicting properties. In Maestro, choose

      TASKS → Browse  Discovery Informatics and QSAR → 3D Field-Based...

If you want to use information on connectivity, you can use fingerprints as the independent variables in Canvas with a variety of fitting methods. You can also use E-state or pharmacophore counts when analyzing R-groups to develop a QSAR model.

You can also construct models based on properties as descriptors, using Strike, via the options in 

TASKS → Browse  Discovery Informatics and QSAR → Property-Based QSAR

in Maestro or in Canvas.

For peptide sequences, you can use the

TASKS → Browse →Biologics Peptide QSAR

panel in the BioLuminate interface to predict peptide properties based on sequence.

To ask a question or get help, please submit a support ticket or email us at help@schrodinger.com.

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