ApoPdb2Receptor

Overview

Converts an apo protein structure into a receptor. The active site is identified by a ligand residue specified by the user (-site_residue). The residue is used as a hint to select most appropriate active site from a list of potential active sites generated by a shape algorithm that searches for pockets/grooves and cavities.

Warning

The input protein structure must be an apo structure. If the protein structure is in a complex with a ligand use the Pdb2Receptor program if the ligand and protein structure are part of a single molecule file, and ReceptorSetup if they have been separated into two files.

Example Commands

Convert 3E1X into receptor

Converts PDB file 3E1X containing an apo protein into a receptor using residue TRP215B to identify the active site.

Input files

  • 3E1X.pdb.gz : PDB file to convert into a receptor.

Command line

prompt> apopdb2receptor -pdb 3E1X.pdb.gz -site_residue TRP215B

Output files

  • receptor.oeb.gz : Receptor version of 3E1X.

Command Line Help

A description of the command line interface can be obtained by executing ApoPdb2Receptor with the --help option.

> apopdb2receptor --help

will generate the following output:

Help functions:
  apopdb2receptor --help simple      : Get a list of simple parameters
  apopdb2receptor --help all         : Get a complete list of parameters
  apopdb2receptor --help defaults    : List the defaults for all parameters
  apopdb2receptor --help <parameter> : Get detailed help on a parameter
  apopdb2receptor --help html        : Create an html help file for this program
  apopdb2receptor --help versions    : List the toolkits and versions used in the application

Required Parameters

-pdb <filename>

A file of an apo protein to be converted into a receptor file. Typically this will be a PDB file, however any molecular format with residue information can be used (e.g., OEBinary).

Warning

The active site must not contain a bound ligand. Use Pdb2Receptor to convert a protein-ligand complex into a receptor file.

[ Aliases = -in ]

-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> HIS
<Residue Name><Residue Number> HIS1034
<Residue Name><Residue Number><Chain ID> HIS1034A

If the residue naming is not specific enough and matches multiple residues in the pdb file the program will list the available, more specific, options to choose from.

[ Aliases = -site ]

Optional Parameters

Receptor Options

-solvent_residues <name> [<name> ...] [Default: HOH]

A list of one or more residue names associated with solvent molecules in the pdb file.

Molecules that have a residue matching one of these names will be stripped from the protein structure and stored in the receptor as extra molecules (i.e., they will have no effect on docking and scoring).

Note

The default setting of this flag (HOH) strips waters from the protein. To not strip any molecules specify this flag as ‘NoSolvents’.

[ Aliases = -solvent ]

Output Options

-receptor <filename> [Default: receptor.oeb.gz]

Name of the output receptor file to generate. The file must be OEBinary (i.e., either a .oeb or .oeb.gz file).

[ Aliases = -rec , -out ]