Jan 4 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
13.7 Make APF Docking SAR Model
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This option allows you to make your own dfa model either on your own data (local table) or from ChEMBL. If the chemicals are not superimposed then this option will automatically superimpose them. If you want to superimpose yourself before running then the chemical superposition options are described here.

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.


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