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PrevICM User's Guide
15.5 Make Chemical Classification Model

This option allows you to make your own kcc models either on your own data (local table) or from ChEMBL.

From your own data:

  • Read in a chemical spreadsheet containing your chemical 2D structure (mol column) and an activity column containing data such as pKd, mM, uM or nM.
  • Select Chemistry/MolScreen/ Make Chemical Classification Model
  • Select the Local Table tab.
  • Give your model a unique name.
  • Find your chemical table from the drop down list.
  • Find the column name containing activity data from the drop down list.
  • Select the activity unit pKd, mM, uM or nM.
  • Select whether you would want pKa charge prediction.
  • Click OK.

From ChEMBL data:

  • Give your model a unique name.
  • Enter a Uniprot ID (e.g. 5ht1f)
  • Select whether or not you want to include all mammalian data or just human.
  • Check makemodel to make the model immediately.

How to use the model to predict:

  • When the model has been built you will see the model listed in the ICM workspace as shown below.

To run the model against a set of chemicals:

  • Read in a chemical spreadsheet containing your chemical data.
  • Right click on the model in the ICM workspace and choose Predict.
  • Enter the table name and prediction model you would like to use.
  • Once the prediction has finished you will see three additional columns: the kcc value, kca value and the Tanimoto distance to the nearest compound in the model dataset.

Custom Model Panel
Make APF/SAR Model

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