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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
Learn and Predict
Docking
 Small Molecule Docking
 Flexible Docking
 Template Docking
 Covalent Docking
 De Novo Tools
 Autofit
 Protein-Protein Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
12.3 Template Docking
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Available in the following product(s): ICM-Pro | ICM-VLS |

To perform constrained docking to a template structure you need to position the template in the desired position in the receptor - this can be done by docking or using the connect option if the template is not already in the correct position. Make sure the template contains only the atoms you wish to match - a template can be edited by right clicking on it in the ICM Workspace and select Edit/ Edit Compound. It is also important to delete hydrogen atoms on the template particulalry in places where substituent groups will be placed.

  • Setup the docking project as described in the Small Molecule Docking chapter.
  • Before starting the docking select Docking/Template
  • Read in the ICM object that you wish to use as a template. Select the template object name in the Object data entry box using the drop down button.
  • Select the template match method. Match by atom name, substructure (option requires that template is an exact substructure of input ligands. If it does not match then no tethers will be imposed for that particular ligand.) , fuzzy (option will find maximum common substructure between template and input ligands. The matched atoms will be tethered during the simulation.) or APF (option will build APF maps of the template and use them in simulation and addition to receptor maps. This options does not require substruture and common substruture between template and input ligands.).

  • Click OK
  • Set the docking job running - Docking/Run Docking Batch


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Covalent Docking

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