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22.5 Cheminformatics Tutorials
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[ Chemical Draw | Edit Chemical | Tutorial - Chemical Searching | Similarity | More Advanced Chemical Similarity Searching | 3D Pharmacophore Searching | 2D Pharmacophore Searching | Chemical 2D to 3D | Convert 2D to 3D from Editor | Convert 2D to 3D from Editor from Table | Conformer Generator | QSAR | Build | Predict | Superimpose Chemicals | How chemical superimpose rigid flexible | Superimpose APF ]

22.5.1 Draw Chemical


Objective

To sketch the chemical structure of Celebrex a COX-2 inhibitor and save it in an ICM Molecular Table.

Background

In ICM it is possible to not only edit structures that you have read into ICM but also create your own and append them to a table, file or a database of structures. All these actions take place in the ICM Molecular Editor.

Instructions

Manual References (Web Links)

Molecular Editor

22.5.2 Edit Chemical


Objective

To edit the Celebrex compound (drawn in the previous example) into a newer C0X-2 drug called Rofecoxib which maintains the Celebrex backbone but with many changes in functionality.

Manual References (Web Links)

Molecular Editor

22.5.3 Chemical Searching


22.5.4 Chemical Similarity Searching


Objective

To find the drugs celebrex and rofecoxib in the chemical table celebrex50.sdf by performing a substructure chemical similarity search.

Background

Using ICM you can perform a compound similarity search whereby a query structure will be searched against a database of compounds. The database can be a compound database already loaded into ICM such as an SDF file or Molsoft's very own compound database called MOLCART.

Instructions

  1. Load the celebrex50.sdf file into ICM (File/Open). This file is provided in the ICM distribution.
  2. Chemistry/Chemical Search
  3. The ICM Molecular Editor and another menu for query search (on the right) will be displayed.
  4. If a molecule is already displayed in the editor you can delete it by Edit/Select All to delete
  5. We will start by seeing if we can identify celebrex and refecoxib from the common substructure shown below. Draw the substructure query using the Molecular Editor buttons. In this example you will draw a benzene ring with a single bond to a Sulfur atom.

* Select the option Local Tables

* Select Celebrex50 as your database.

* Select substructure search

* Select the other options as shown in the figure above. You can experiment with different values from the drop down menu.

* Select the Search button.

* A new table will be constructed called result1 with your substructure search results contained in it. If you added Rofecoxib to the celebrex50.sdf in the previous example your results table should contain 2 hits - celebrex and rofecoxib.

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Notes and Things to Try:

Manual References (Web Links)

Chemical Substructure/Similarity Searching

22.5.5 Advanced Chemical Similarity Searching


Objective

To use the right click options in the chemical search window to add additional search criteria and find ways to distinguish Celebrex from Rofecoxib.

Instructions

  1. Load the celebrex50.sdf file into ICM (File/Open). This file is provided in the ICM distribution. Add Rofecoxib to the celebrex50.sdf file as described in the chemical-edit tutorial.
  2. Chemistry/Chemical Search
  3. The ICM Molecular Editor and another menu for query search (on the right) will be displayed.
  4. If a molecule is already displayed in the editor you can delete it by Edit/Select All to delete
  5. Follow the search instructions described in the previous example with the following chemical search substructures:

Celebrex contains halogen atoms and Rofecoxib does not - therefore one way to distinguish the two would be a simple filter as shown below.


One of the key features between Celebrex and Rofecoxib is a benzene ring connected to a five-membered ring. The difference is that in celebrex the connection point is with a nitrogen atom and in Rofecoxib the connection point is with a carbon atom. Therefore to retrieve both Celebrex and Rofecoxib in the results table you would need to right click and select Element/Any (*) and select Ring Size 5 (r5) or to retrieve only one you would need to specify nitrogen or carbon at the connection point.

You can also perform the same query using Ring Membership (R1) or Attachment Point.

Manual References (Web Links)

Chemical Similarity Searching

22.5.6 3D Pharmacophore Searching


Objective Undertake a 3D pharmacophore search of a table containing 3D coordinates.

Manual References (Web Links)

3D Pharmacophore Search

22.5.7 2D Pharmacophore Searching


Objective Undertake a 2D pharmacophore search of a chemical spreadsheet.

Manual References (Web Links)

2D Pharmacophore Search

22.5.8 How to Convert Chemicals from 2D to 3D


22.5.9 How to convert 2D sketches in the molecule editor into 3D.


22.5.10 How to convert 2D chemical sketches to 3D.


22.5.11 How to generate 3D ligand conformers.


22.5.12 How to Build and Apply QSAR Prediction Models


22.5.13 How to build a QSAR prediction model.


22.5.14 How to apply a QSAR prediction model.


22.5.15 How to Superimpose Chemicals


22.5.16 How to Perform Rigid and Flexible Chemical Substructure Superposition.


22.5.17 How to use Atomic Property Fields for Chemical Superposition



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