Ligandable Medoids Extraction

Quick floe search term: CPD C3

This floe can only be run with the output generated by one of the cryptic pocket analysis floes (Probe Occupancy Analysis, Dynamic Probe Binding Analysis, and Exposon Analysis Floes).

Tip

This floe typically takes 5 minutes to run and costs ~$1.

Search and Run the Floe in Orion

Locate the Floe in Orion

Navigate to the Floe page using the blue navigation bar.

On the Floe page, click on the Floes Tab, where you will find a list of the available floes and packages.

Under the Category Floe Filters on the left, click on the caret next to the Packages filter to expand the list of packages and click on the OpenEye Cryptic Pocket Detection Floes package. This will ensure that the floes listed in the middle of the page are from this package.

From this list, click on the Ligandable Medoids Extraction Floe and then click the blue “Launch Floe” button to launch the Job Form.

Provide Input Files and Parameters to Run the Floe

• Output path:

  Select the destination for your output data by specifying the Output path.

• Pocket Receptors:

  You will need to provide a Pocket Receptors dataset generated by one of the cryptic pocket analysis floes (Probe Occupancy Analysis, Dynamic Probe Binding Analysis, Exposon Analysis, or Combined Probe Binding Site Analysis Floe) as an input.

• Medoids Trajectory:

  You will need to provide a Medoids Trajectory dataset generated by one of the cryptic pocket analysis floes (Probe Occupancy Analysis, Dynamic Probe Binding Analysis, Exposon Analysis, or Combined Probe Binding Site Analysis Floe) as an input. This dataset and the “Pocket Receptors” dataset must be generated by the same job.

• Ligandability score cutoff:*

  This is the normalized ligandability score cutoff used for selection of the medoid conformations. Medoid conformations with normalized ligandability above this cutoff value will be outputted. If the cutoff is set to 0.0, pocket receptors for all medoid conformations will be outputted for selected pocket rank.

• Pocket Rank:

  Pocket ranks for which ligandable medoids need to be extracted. Enter the pocket ranks. If this is left empty, the ligandable medoids will be outputted for the highest tanking pocket in the input Pocket Receptors dataset.

Figure 1. Job Form for the Ligandable Medoids Extraction Floe.

Click on the green “Start Job” button.