Induced-Fit Posing (IFP) Prep: Pruning reference receptor for docking [IFP]

Category Paths

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

  • Product-based/OEDocking

  • Product-based/Molecular Dynamics/GROMACS

  • Product-based/Molecular Dynamics/OpenMM

  • Role-based/Computational Chemist

  • Role-based/Medicinal Chemist

  • Solution-based/Hit to Lead

  • Task-based/Ligand Posing & Analysis


  • Purpose:

    • This Floe prunes the sidechains in the binding site of the reference receptor for docking. The output datasets can be used as “Optional Pruned Reference Receptor Input Dataset” in the “Optional Inputs” section of the “Induced-Fit Posing (Confined)” Floe.

  • Input Requirements:

    • The reference receptor needs to have a unique OEReceptor.

  • Limitations:

    • The input reference protein dataset must contain a bound ligand (An apo state of the reference is not supported in this Floe).

    • The Floe takes a single reference receptor at a time.

  • Expertise Level:

    • Intermediate/Advanced

  • Compute Resource:

    • Low

  • Keywords:

    • IFP, Induced-Fit Posing, Induced Fit Posing, IFD, Induced-Fit Docking, Induced Fit Docking

Promoted Parameters

Title in user interface (promoted name)

Reference Receptor Active Site Pruning Parameters

Pruning all active site residues (prune_all_as_res): If On, it will ignore the solvent exposed area threshold and prune all binding site residues to ALA

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Cut-off distance (dist_from_lig): Cut-off distance to define the binding site

  • Type: decimal

  • Default: 5.0

Solvent Exposed Area Threshold (area_threshold): Solvent exposed area threshold (in square Angstrom). Binding site residues with solvent exposed area higher than the threshold will be pruned to ALA

  • Type: decimal

  • Default: 1