Example Commands

Basic Hybrid Docking Example

This example hybrid docks molecules using a single processor.

Input files

  • receptor.oeb.gz :
    A receptor file containing the structure of the target protein and a bound ligand. (see Receptor Preparation section).
  • multiconformer_ligands.oeb.gz :
    Conformationally expanded 3D ligands to dock. (see Ligand Preparation section).

Command line

prompt> hybrid -receptor receptor.oeb.gz -dbase multiconformer_ligands.oeb.gz

Output files

  • hybrid_docked.oeb.gz : Top 500 scoring molecules of multiconformer_ligands.oeb.gz docked into receptor.oeb.gz.
  • hybrid_undocked.oeb.gz : Molecules of multiconformer_ligands.oeb.gz that could not be docked into the active site (generally occurs if the molecules are too big for the site). This file will not be present if all molecules were successfully docked to the active site.
  • hybrid_score.txt : A tab separated text file containing the name and score of each of the top 500 ligands.
  • hybrid_report.txt : A text report of the docking process.
  • hybrid_settings.param : A text file containing the parameters used for this run.
  • hybrid_status.txt : A text file that is overwritten periodically during the run with the status of the run.

Hybrid Docking with Multiple Crystal Structures

In this example HYBRID docks molecules using multiple structures of the target protein.

Input files

  • receptor1.oeb.gz :
    A receptor file containing the structure of the target protein and a bound ligand. (see Receptor Preparation section).
  • receptor2.oeb.gz :
    A receptor file containing the structure of the second target protein and a bound ligand. This receptor file should have a different structure of the same target protein in receptor1.oeb.gz, generally with a different bound ligand. (see Receptor Preparation section).
  • multiconformer_ligands.oeb.gz :
    Conformationally expanded 3D ligands to dock. (see Ligand Preparation section).

Command line

prompt> hybrid -receptor receptor1.oeb.gz \
               -receptor receptor2.oeb.gz \
               -dbase multiconformer_ligands.oeb.gz

Output files

  • hybrid_docked.oeb.gz : Top 500 scoring molecules of multiconformer_ligands.oeb.gz docked into either receptor1.oeb.gz or receptor2.oeb.gz. The title and filename of the receptor docked to will be tagged to the SD data of each docked ligand (see the report.txt file).
  • hybrid_undocked.oeb.gz : Molecules of multiconformer_ligands.oeb.gz that could not be docked into the active site (generally occurs if the molecules are too big for the site). This file will not be present if all molecules were successfully docked to the active site.
  • hybrid_score.txt : A tab separated text file containing the following information for each of the top 500 ligands.
    • Name of the ligand
    • Score of the ligand
    • Title of the receptor site the ligand docked to.
    • Filename of the receptor site the ligand docked to.
  • hybrid_report.txt : A text report of the docking process.
  • hybrid_settings.param : A text file containing the parameters used for this run.
  • hybrid_status.txt : A text file that is written periodically during the run with the status of the run.

MPI docking example

In this example HYBRID docks molecules to a single receptor on 4 processors of the host machine.

Input files

  • receptor.oeb.gz :
    A receptor file containing the structure of the target protein and a bound ligand. (see Receptor Preparation section).
  • multiconformer_ligands.oeb.gz :
    Conformationally expanded ligands to dock. (see Ligand Preparation section).

Command line

prompt> hybrid -mpi_np 4 -receptor receptor.oeb.gz \
                              -dbase multiconformer_ligands.oeb.gz

Output files

  • hybrid_docked.oeb.gz : Top 500 scoring molecules of multiconformer_ligands.oeb.gz docked into receptor.oeb.gz.
  • hybrid_undocked.oeb.gz : Molecules of multiconformer_ligands.oeb.gz that could not be docked into the active site (generally occurs if the molecules are too big for the site). This file will not be present if all molecules were successfully docked to the active site.
  • hybrid_score.txt : A tab separated text file containing the name and score of each of the top 500 ligands.
  • hybrid_report.txt : A text report of the docking process.
  • hybrid_settings.param : A text file containing the parameters used for this run.
  • hybrid_status.txt : A text file that is overwritten periodically during the run with the status of the run.