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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
Molecular Dynamics
MolScreen
 Load Models and Run
 Results Table
 Model Types
 Custom Model Panel
 Make Classification Model
 Make APF/SAR Model
 Predict Metabolic Oxidation
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
15.5 Make Chemical Classification Model
Next

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 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.


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