Article ID: 337 - Last Modified: November 7, 2011
Is there an efficient way to filter ligands from a docking run that only make specific key interactions? These key interactions are either determined by examining the results, or through knowledge of known binders.
You can apply the SIFT (Interaction Fingerprints) tools to the results of a docking run in order to view the key interactions in the form of a interactive histogram plot. The plot can be generated for entries in the Project Table (unknown compounds from a docking run, and or known inhibitors). The first entry in the Table is the protein, and the subsequent entries the ligands.
Open the Interaction Fingerprints panel via Scripts → Cheminformatics → Interaction Fingerprints.
Include all interactions, Generate Fingerprints, and display the Interaction Matrix. The plot itself is self-explanatory, and interactive. If the data contained both known and unknown inhibitors, you can easily make the distinction between the kind of interactions made by studying the continuity of the bars in the plot. The bars shown along the top of the main plot allow you to easily identify the compounds back in the Project Table and you can export them from there.
For example, if you're only interested in ligands that make GLN123, ASP124 and GLY145 you can easily find these ligands by switching one option in the SIFT window. Switch from "Picking in plot performs" to "Selection" and this will allow you to control-click on the bars in the upper histogram. This will select ligands in the Project Table that interact with any of the selected residues. Once they are selected a normal export from the PT will save them to a file.
An alternative is to use the Pose Filter panel (Scripts → Docking Post-processing → Pose Filter). In this panel you can define the interaction that the ligand makes with the receptor and choose the receptor residues that it interacts with. The filter can be applied to ligands that have all the interactions (AND) or to ligands that have any of the interactions (OR).
Keywords: glide, docking, key-interactions, filter, known-inhibitors, Maestro
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