HYBRID docks molecules using a single receptor or using multiple structures of the
target protein. When using a single structure, the input files are simply the receptor
and the ligand database. However, when using multiple structures of the target protein,
the input files are all of the receptor files and the ligand database.
- receptor1.oeb.gz - a receptor file containing the structure of the target protein
and a bound ligand.
- 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.
- multiconformer_ligands.oeb.gz - conformationally expanded 3D ligands to dock.
Setting up and running a HYBRID job is exactly like setting up and
running a FRED job.
To dock a set of ligands into the receptor 2IKO_receptor.oeb.gz:
> hybrid -receptor 2IKO_receptor.oeb.gz -dbase all.oeb.gz
By default, HYBRID generates several output files. Unless you specify a different
Output prefix during setup, HYBRID will use the prefix chapter_hybrid for all output files.
- hybrid_docked.oeb.gz - top 500 scoring molecules of all.oeb.gz docked into 2IKO_receptor.oeb.gz.
- hybrid_undocked.oeb.gz - molecules of all.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 written periodically during the run with the
status of the run.
If you have a multi-processor machine, you can use the OpenMPI option.
> hybrid -mpi_np 4 -receptor 2IKO_receptor.oeb.gz -dbase all.oeb.gz -prefix 2IKO_hybrid
As with the output from FRED docking runs, HYBRID results may be
viewed and analyzed in VIDA as shown in figure 2IKO HYBRID DOCKED.
2IKO HYBRID DOCKED results showing the reference ligand (green) and the top docked ligand
Likewise, you also can create a summary PDF report for the HYBRID results using DockingReport.