SPRUCE - Import Prepared PDB Files

Category Paths

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

  • Role-based/Computational Chemist

  • Product-based/SPRUCE

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation

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

Description

This floe uses Spruce to generate an OEDesignUnit object used by downstream OpenEye modeling applications in Orion, such as docking, posit, gameplan, or short-trajectory MD.

The required input for this floe is PDB and/or MMCIF files that have already been prepared for modeling applications outside of Orion. Required preparation steps for downstream applications are, to name a few, enumerated or collapsed alternate locations, explicit and optimized hydrogen atoms, properly treated terminal residues (either charged or capped), .

If a ligand cannot be detected during the run, consider specifying the ligand residue name, increasing the size of the input variable “max_residues”, given as an optional input to this floe. Or if this is a known apo structure, you can provide the definition of a residue in the binding site.

You can read more about Spruce in the toolkit documentation.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Input structure (PDB/MMCIF) files (structure_inp_files):

  • Required

  • Type: file_in

Outputs

Output Dataset (dataset_data_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Spruce_prep_dataset

Output Dataset (failed_data_out): Output dataset to write to

  • Required

  • Type: dataset_out

  • Default: Failed_Spruce_prep_dataset

Ligand Parameters

Ligand Name(s) (ligand_names): format 3-letter codes e.g. ‘LIG’, for peptides separate codes with dashes (e.g. ‘SER-VAL-TPO-ALA’.

  • Type: string

Strict Ligand (strict_ligand): Option to only emit design units with ligands that match the ligand names (if any are provided)

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Ligand Type (lig_type): The type of ligand that is expected for the system. Affects the max/min atom counts and the max residue count (if applicable) for the ligand in the system. Overrides can be individually input. Defaults are as follow: Small Molecule: min_atoms=8, max_atoms=100, max_residues=5; Peptide: min_atoms=8, max_atoms=200, max_residues=2; Macrocycle: min_atoms=8, max_atoms=250, max_residues=20; Fragment: min_atoms=2, max_atoms=35, max_residues=5

  • Required

  • Type: string

  • Default: Small Molecule

  • Choices: [‘Small Molecule’, ‘Peptide’, ‘Macrocycle’, ‘Fragment’]

Un-liganded Structure Parameters

Enumerate pockets (enum_pocket): Option to enumerate pockets when no ligand is found

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Site Residue Entry (site_residue): Single site residue specification for APO structures. 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