Ligandable Medoids Extraction

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

Description

This floe extracts ligandable medoids for selected pockets.

Promoted Parameters

Title in user interface (promoted name)

• Ligandability Score Cutoff (ligandability_score_cutoff) type: decimal: Normalized ligandability score cutoff for selection of medoids. Medoid conformations with normalized ligandability above this cutoff value will be outputted.

  Default: 0.27 , Max: 0.7
• Ligandable Medoids (ligandable_medoids_dataset) type: dataset_out: A dataset containing ligandable medoids for selected cryptic pockets.

  Default: Ligandable Medoids dataset
• Pocket Rank (selected_pocket_ranks) type: integer: Pocket ranks for which ligandable medoids need to be extracted. If left empty, the ligandable medoids will be outputted for the highest ranking pocket in the input “Pocket Receptors” dataset.

Titles of required parameters (promoted names)

• Medoids Structures (data_in) type: data_source: Dataset containing medoids structures outputted by cryptic pocket analysis floes.
• Pocket Receptors (data_in) type: data_source: Dataset containing cryptic pocket receptors outputted by cryptic pocket analysis floes.

Optional parameters (promoted names)

• Ligandability Score Cutoff (ligandability_score_cutoff) type: decimal: Normalized ligandability score cutoff for selection of medoids. Medoid conformations with normalized ligandability above this cutoff value will be outputted.

  Default: 0.27 , Max: 0.7
• Pocket Rank (selected_pocket_ranks) type: integer: Pocket ranks for which ligandable medoids need to be extracted. If left empty, the ligandable medoids will be outputted for the highest ranking pocket in the input “Pocket Receptors” dataset.
• Ligandable Medoids (data_out) type: dataset_out: A dataset containing ligandable medoids for selected cryptic pockets.

  Default: Ligandable Medoids dataset