ICM Manual v.3.9
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2020, Molsoft LLC
Feb 15 2024

Contents
 
Introduction
Reference Guide
Command Line User's Guide
 ICM-shell
 ICM graphics
 Str.Analysis
 Sequence
 Molcart
 Pharmacophores
 Energy
 Molecules
 Animation
 Symmetry
 X-ray
 Plotting
 Docking/VLS
 Examples
 _chemSuper
 PROTAC Modeling
 Chemical Conformation Generator
 RIDE
References
Glossary
 
Index
PrevICM Language Reference
Chemical Superposition using APF - Ligand Based Screening
Next

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.

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. 

Prev
Diverse subset
Home
Up
Next
PROTAC Modeling

Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2024, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC.