Build Sidechains

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 uses Spruce function OEBuildSidechains to build partial amino acid residues. The required input is a dataset with an OEDesignUnit.

Promoted Parameters

Title in user interface (promoted name)

Sidechain Building Options

Rotamer Library (rot_lib): Rotamer library to use for side-chain building.

  • Required

  • Type: string

  • Default: Richardson2016

  • Choices: [‘Dunbrack’, ‘Richardson’, ‘Richardson2016’]

Delete Clashing Solvent (del_solvent): The sidechain builder will remove a water if it clashes with built piece.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Rotamer Coverage (rot_coverage): Limits the number of rotamers checked for each residue type, based on frequency.

  • Required

  • Type: decimal

  • Default: 100.0

Build Residues (build_residues): Build these specific residues. 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. Separate multiple with ‘|’ delimiter.

  • Type: string

Add hydrogens to DU (add_hydrogen switch): If off, then the DU will not be (re-)protonated. If on, then missing hydrogens are protonated and partial charges will be recomputed.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]