Enumerate Pockets on Design Units

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 (to avoid leaving this page, right-click and open link in new tab). This floe allows for one or both methods to be run.

Potential Input Sources SPRUCE (to avoid leaving this page, right-click and open link in new tab), SPRUCE - Protein Preparation

Promoted Parameters

Title in user interface (promoted name)

Pocket Finding Options

Use OEPocket Finding (run_oepocket): Option to use OEPocket to generate design units.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Use F-Pocket Finding (run_fpocket): Option to use f-pocket to generate design units.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Min surface area (min_surf_area): Option to set minimum surface area for pocket finding.

  • Required

  • Type: decimal

  • Default: 150.0

Max surface area (max_surf_area): Option to set maximum surface area for pocket finding.

  • Required

  • Type: decimal

  • Default: 3000.0

Site Residue Entry (site_residue): Single site residue specification used to filter discovered pockets. Format: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard.

  • Type: string