Command Line OverviewΒΆ

This OEDocking distribution contains a suite of command line programs. The three primary programs are FRED, HYBRID and POSIT that dock molecules into a receptor site using either traditional or hybrid docking. The remaining programs are either for preparing the active site or analyzing the docked poses.

Program Function Description
fred Docking Docks molecules.
hybrid Docking Docks molecules and uses the structure of a bound ligand to guide the docking.
posit Docking Docks molecules and compares predicted poses to observed bound ligands in related co-crystals.
scorepose Rescoring Rescores and optional optimizes poses in an active site with fred’s scoring function.
docking_report Molecule Report Creates a PDF report for one or more docked molecules.
pdb2receptor Protein Prep Creates a receptor from a pdb file with a protein-ligand complex.
apopdb2receptor Protein Prep Creates a receptor from a pdb file with an apo protein.
receptor_setup Protein Prep Creates a receptor from a protein structure and either a bound ligand or a box enclosing the active site.
receptor_toolbox Protein Prep A utility program for receptors that reports information about a receptor and can make simple edits of the receptor.
combine_receptors Protein Prep Makes a single receptor using multiple ligands that may be a better target for predicting some ligands.


FRED, HYBRID, POSIT and SCOREPOSE are multiprocessor enabled via MPI on supported platforms.