Jan 18 2018 Feedback.
Contents
 
Introduction
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
Virtual Screening
MolScreen
 Model Types
 Brief Panel
 Full Model Panel
 Custom Model Panel
 Results Table
 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
13.6 Make Chemical Classification Model
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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 immeditately.

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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