ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Jun 5 2024

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Chemical Superposition using APF - Ligand Based Screening

Flexible chemical superposition onto one or several rigid templates using Atomic Property Fields(APF)

The Atomic Property Fields (APF) superposition/alignment method is published here. In 2010, Giganti et al reported on the high accuracy of ICM APF screening compared to other ligand-based methods.


icm _chemSuper templates.ob|sdf input.sdf|inx|molt output.ob|sdf [options] [effort=(1.)]

Flexible chemical superposition of chemicals from the input database to one or several rigid templates using Atomic Property Fields Options (recommended are marked):

  • -c : Charge ionizable groups according to built-in pKa model (VLS mode) (*)
  • -d : cis-trans sampling
  • -e : penalize atoms outside the Envelope of the template(s)
  • -F : calculate MMFF strain
  • -fo: Fix Omega angles (peptide bond angles)
  • -m : keep Multiple alternative poses
  • -M : write APF maps derived from the input compounds and MODEL table to a file (/tmp/output.icb)
  • -O : score Only, poses taken directly from input without sampling
  • -o : downweight contributions from template atoms by Occupancy
  • -r : sample Rings
  • -R : Rigid superposition
  • -S : output columns with the APF Score components
  • -s : output a column with the APF Score (*)
  • -t : sample Tautomers
  • -v : verbose: print commands
  • -shape : match shape only
  • APFcutoff= : skip compounds with APF score above cutoff (VLS mode)
  • effort=(1.) : simulation duration factor.Use 3 to 20 for a serious screen
  • proc=(1) : number of parallel jobs to launch
  • exclude= : excluded volume points
  • from= to= : screen a section of the input database (parallelized VLS mode)
  • radius=(1.2): APF smearing radius
  • weight=(3.) : APF weight (vs the energies)
  • Xweight=(3.) : repulsion weight of the 'eXcluded volume' atoms


icm _chemSuper threedrugs.sdf drugbank.sdf /tmp/output.sdf -s -F -c effort=5. 

Diverse subset
PROTAC Modeling

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