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Contents
 
Introduction
Help Videos
Reference Guide
Getting Started
Protein Structure
Molecular Graphics
Slides & ActiveICM
Sequences & Alignments
Protein Modeling
Cheminformatics
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 Chemical Spreadsheets
 Editor
 Chemical Search
 2D Interaction
 Convert to 3D
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 Calculate Properties
 Standardize Table
 Annotate
 Align/Color by 2D Scaffold
 Formal Charges
 Enumerate Formal Charge States
 Convert
 Build Prediction Model
 Predict
 Generate 3D Conformers
 Generate Tautomers
 Generate Stereoisomers
 Prodrug
 Ligand Energetics
 Cluster Set
  Chemical clustering
  Center
  Re-order and Distance
  Edit tree
  Auto Close
  Max Common Substructure
  R-Group Decomposition
 PCA Analysis
 Visualize Chemical Space
 Compare Two Sets
 Merge Two Sets
 Select Duplicates
 MPO
 Combinatorial Chemistry
 SAR Analysis
 Chemical Superposition
 APF Superposition
 APF Tools
Learn and Predict
Docking
Virtual Screening
MolScreen
3D Ligand Editor
Tables and Plots
Local Databases
ICM-Scarab
KNIME
Tutorials
FAQs
 
Index
PrevICM User's Guide
10.25 Cluster Set
Next

[ Chemical clustering | Center | Re-order and Distance | Edit tree | Auto Close | Max Common Substructure | R-Group Decomposition ]

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

Clustering is described in more detail in the Tables Clustering section of this manual. To undertake chemical clustering choose:

  • Chemistry/Cluster Set

10.25.1 How to perform chemical clustering.


10.25.2 How to select representative centers from a tree.


10.25.3 How to reorder branches and change the distance of trees.


10.25.4 How to edit the tree - labels, spacing and coloring.


10.25.5 Auto Close Tree Mode


To make working with large cluster trees a little easier you can activate the auto close mode which will close downstream clusters and make them more compact.

To do this:

  • Right click in white space on the cluster and choose Preferences.
  • Select "Auto Close Clusters Downstream".

10.25.6 Calculate Maximum Common Substructure for Nodes


To calculate the Maximum Common Substructure (MCS) for nodes in a treee:

  • Chemistry/Cluster Set
  • Select the option Calculate Maximum Common Substructure for Nodes
  • Hover over a node to view the MCS.
  • Right click on a node and choose "Extract Maximum Common Substructure" to extract it to a table.

10.25.7 R Group Decomposition from Clustering Node


To perform R-group decomposition directly from a cluster node:

  • Chemistry/Cluster Set
  • Select the option Calculate Maximum Common Substructure for Nodes.
  • Hover over a node to view the MCS.
  • Right click on a node and choose "R-group decomposition for node".

The resulting table can be used for R-Group Enumeration or SAR.


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