ICM Manual v.3.7
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2013, Molsoft LLC
May 16 2013
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.
_chemSuper template.ob|.sdf input.sdf|.inx output.ob|sdf [options] [radius=(1.2)] [thoroughness=(1.)]
- -r : sample rings"
- -R : rigid superposition"
- -d : cis-trans sampling"
- -F : calculate MMFF strain"
- -S : output columns with the APF score components"
- -s : output a column with the APF score"
- -m : keep multiple alternative poses"
- -O : score only, poses taken directly from input without sampling"
- -o : downweight contributions by occupancy"
- -e : penalize atoms outside the envelope of the template(s)"
- -t : sample tautomers"
- -c : charge ionizable groups according to built-in pKa model (VLS mode)"
- exclude= : excluded volume points"
- Xweight=(3.) : repulsion weight of the 'excluded volume' atoms"
- APFcutoff=CUTOFFVALUE : output only compounds with the APF score better than specified cutoff (VLS mode)"
- from= to= : go through the segment of the input database (parallelized VLS mode)"