Spruce4Docking

Overview

Spruce4Docking is a utility program for preparing either a protein-ligand complex , an apo target, or separate protein and ligand files into receptors. The input can be in PDB, MMCIF, or any fileformat that includes residue information (e.g. OEB). The ligand will be autodetected if present, but its name can be specified on the command line if multiple potential ligands are present. The created receptor will contain the specified bound ligand. For an apo structure a site-residue or box can be specified to indicate the binding site location.

Note

While Spruce4Docking is good at automatically setting up receptors, it is recommended that the MakeReceptor GUI be used to examine/modify the receptor created by Spruce4Docking prior to using it with FRED, HYBRID or POSIT. Particularly, if a user wants to define constraints or include specific water molecules in the receptor. This step is not required, however.

Example Commands

Prepare and convert PDB/MMCIF file 6FJT into receptor

Prepares and converts PDB file 6FJT into a receptor, auto detecting the ligand to be DKQ. Input could also have been MMCIF.

Input files

  • 6FTJ.pdb.gz : PDB file to prepare and convert into a receptor.

Command line

prompt> spruce4docking 6FTJ.pdb.gz

Output files

  • rec_6FTJ_HIL__DU__DKQ_H-303.oeb.gz : Receptor version of 6FTJ pdb complex.

Command Line Help

A description of the command line interface can be obtained by executing Spruce4Docking with the --help option.

> spruce4docking --help

will generate the following output:

Help functions:
  spruce4docking --help simple      : Get a list of simple parameters
  spruce4docking --help all         : Get a complete list of parameters
  spruce4docking --help defaults    : List the defaults for all parameters
  spruce4docking --help <parameter> : Get detailed help on a parameter
  spruce4docking --help html        : Create an html help file for this program
  spruce4docking --help versions    : List the toolkits and versions used in the application

Required Parameters

-in <filename>

Either a PDB or MMCIF file containing a protein-ligand complex or an apo protein. Any file format with residue information can be used (.e.g OEB); The structure will then be prepared with spruce and converted into a docking receptor.

[keyless parameter 1]

Optional Parameters

Input Options

-map <filename>

A MTZ file containing the electron density map. This enables an evaluation of the Iridium category, and will also result in sorted receptors based on the Iridium data.

-max_lig_residues

Maximum number of residues to be detected as a ligand, default is 5. Primarily needs to be set for larger peptidic ligands.

Output Options

-prefix <prefix>

Name of the output receptors files is based on the spruce design unit filename, this specifies the prefix for those filenames.

-log <logfile>

The argument for this flag specifies the name of the log file. This overrides any specified prefix. The default will be spruce4docking_output.log, if no prefix is specified.

-settings <settingsfile>

The argument for this flag specifies the name of the settings file. This overrides any specified prefix. The default will be spruce4docking_settings.param, if no prefix is specified.

Ligand Specification Options

-ligand_names <ligand name>
If spruce does not autodetect the ligand or multiple ligands are detected, this parameter can be used to assist in the ligand detection.
Form Example
<Residue Name> “LIG”
<Residue Name> “ALA-VAL-TYS-PHE-GLU”
-bound_ligand <ligand_file>

Bound ligand molecule file if not in the input structure

Apo Site Specification Options

-site_residue <residue identifier>

The name of a residue near the active site of the protein. Residue names can be of the following forms.

Form Example
<Residue Name>:<Residue Number>:<InsertCode>:<Chain ID> “ASP:25: :A”
-box <box file> [No Default]

A file describing a box enclosing the active site. All docked poses will be required to fit within this box.

The box must be in a 3D molecular format. SDF, MOL2, OEBinary and several other common molecular formats are supported.

The box will always be aligned along the X, Y and Z axis of the coordinate system and the edges of the box will be the maximum and minimum X, Y and Z value of any atom in the box file.

Note

This flag cannot be specified with -bound_ligand

-addbox <distance> [No Default]

This flag adjusts the box created by the -box flag by extending each edge of the box by the specified number of Angstroms. Thus each dimension of the box will be enlarged by twice the setting of this parameter.

If -box is not specified this flag has no effect.

Receptor Options

-strip_water [Default: true]

If this flag is set to true then waters will automatically be stripped from the protein and stored as extra molecules.

-no_preparation [Default: false]

Flag can be set to true if input structure has been prepared elsewhere. If this flag is set to true the structure will no be prepared, meaning no hydrogens will be added, missing side-chains rebuilt, or chain breaks capped.