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.

Syntax:

 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

Example:

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