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13.3 Ligand-Based Screening using APF 3D Pharmacophores

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

This option allows you to perform a ligand-based screen using the Atomic Property Fields (APF) of superimposed chemicals. SD files are screened and the ligands are scored according to their fit into the APF field. Read more about APF here: http://www.molsoft.com/apf.html

Read in and display the superimposed template chemicals. In this example we will use three aldose reductase crystal structures 1PWM, 2I17, and 1Z8A. IMPORTANT: Convert each PDB file to an ICM object.

Select each chemical you wish to contribute to the APF fields. Select by double clicking on the chemical in the ICM workspace and hold down the CTRL key.

Choose the Screen SD file against template molecule(s) option. Chemistry/APF tools/Screen SD file against template molecule(s)

Select the SD database you wish to screen.
  • Select the database in SD format you wish to screen and
  • Select whether you want flexible rings to be sampled by checking the appropriate box.
  • Select whether you want cis and trans conformations of double bonds to be sampled by checking the appropriate box.
  • Select whether you would like to sample tautomers.
  • A score for how well the ligand fits into the APF envelope can be generated. Select if desired.
  • Scores <-100 are generally good and so you can filter out poor ligands using the Keep only Score < option.
  • Select the Advanced button if you want the superposition to be weighted by occupancy of the atoms by checking the appropriate box. It is often desirable to preferentially superimpose parts of a ligand while ignoring other regions. This can be achieved by setting the occupancy to zero for regions you are not focusing on. See: command line manual http://www.molsoft.com/man/icm-commands.html#set-occupancy . You can also define the weights for lipophilic and polar matches.

A notification will be displayed when the screen is completed.Click OK and a hitlist table will be displayed.

A hitlist table will be displayed. You can sort the table by score and toggle the display on and off using the buttons in the L column.

Fragment Screening

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