Enumerate Pockets on Design Units

Category Paths

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

  • Product-based/SPRUCE

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation

Description

This floe runs pocket finding on input Design Unit(s). Each pocket is enumerated into its own OEDesignUnit with the binding site set as the discovered pocket.

Two methods can be use for pocket finding: OEPocket](https://docs.eyesopen.com/toolkits/python/sprucetk/OESpruceClasses/OEPocket.html) (to avoid leaving this page, right-click and open link in new tab) and [fpocket. This floe allows for one or both methods to be run.

Potential Input Sources SPRUCE, SPRUCE - Protein Preparation

Promoted Parameters

Title in user interface (promoted name)

  • Max surface area (max_surf_area) type: decimal: Option to set maximum surface area for pocket finding.
    Default: 3000.0
  • Min surface area (min_surf_area) type: decimal: Option to set minimum surface area for pocket finding.
    Default: 150.0
  • Use F-Pocket Finding (run_fpocket) type: boolean: Option to use f-pocket to generate design units.
    Default: True
  • Use OEPocket Finding (run_oepocket) type: boolean: Option to use OEPocket to generate design units.
    Default: True

Titles of required parameters (promoted names)

  • Output Dataset (data_out) type: dataset_out: Dataset with modelled design unit.
    Default: EnumeratePocketsOnDesignUnit
  • Failure Dataset (data_out) type: dataset_out: Dataset with design unit that failed to be successfully modelled.
    Default: failed_EnumeratePocketsOnDesignUnit
  • Input Design Unit (data_in) type: data_source: Dataset with design unit(s) to be modelled

Optional parameters (promoted names)

  • Max surface area (max_surf_area) type: decimal: Option to set maximum surface area for pocket finding.
    Default: 3000.0
  • Min surface area (min_surf_area) type: decimal: Option to set minimum surface area for pocket finding.
    Default: 150.0
  • Use F-Pocket Finding (run_fpocket) type: boolean: Option to use f-pocket to generate design units.
    Default: True
  • Use OEPocket Finding (run_oepocket) type: boolean: Option to use OEPocket to generate design units.
    Default: True