ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2018, Molsoft LLC
Jan 4 2018

Contents
 
Introduction
Reference Guide
Command Line User's Guide
 ICM-shell
 ICM graphics
 Str.Analysis
 Sequence
 Molcart
 Pharmacophores
  Ph4 object faq
 Energy
 Molecules
 Animation
 Symmetry
 X-ray
 Plotting
 Docking/VLS
 Examples
 _chemSuper
 Chemical Conformation Generator
References
Glossary
 
Index
PrevICM Language Reference
Pharmacophores
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[ Ph4 object faq ]

ICM can define a specialized object that can be used to as a generalized description of several ligands binding to the same pocket (a pharmacophore), or a fragment of the binding surface.

Pharmacophore object


A pharmacophore object, in contrast to regular atomic objects contains disconnected "centers" representing different interaction types and chemical fragments oriented in space.

Here are the main characteristics of the ICM pharmacophore objects.

  • ICM pharmacophore objects are non-ICM objects and have special type called "pharma" or "ph4", to set this type use the set type object (e.g. set object a_ "ph4") .
  • The objects contain a mixture of the chemical fragments and single atom centers (a.k.a. pharmacophore spheres).


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