Overview

The OEDocking suite contains three docking programs, FRED, HYBRID and POSIT, and associated utilities. The input to FRED, HYBRID or POSIT is one (or more) crystallographic structures of the target protein (possibly including the co-crystallized ligand) and one or more drug-like molecules to be docked. The output is the docked structure of the molecules and information about the score or confidence in the docked structure.

At the end of these tutorials, you will be able to run:

• SPRUCE to prepare receptor files from PDB or MMCIF files for docking.

• COMBINE_RECEPTORS to take disparate but sequence related proteins and combine the complexes into new receptors with more thorough binding information.

• FRED to dock multi-conformer molecules into the structure of a target protein and score the molecules.

• HYBRID to dock multi-conformer molecules into the structure(s) of a target protein and the structure of a bound ligand and score the molecules.

• POSIT to generate potential poses of ligands against OEDocking receptor targets.

• DOCKING_REPORT to generate a PDF report for one or more molecules docked by FRED , HYBRID or POSIT.

The basic workflow for docking ligands using FRED, HYBRID or POSIT is as follows:

• Generate OEDocking receptors with bound ligands.

• Dock ligands into receptor.

• Analyze results.

Note

Data for the tutorials is included in the application bundle. Please see Example and Tutorial Data for platform specific information regarding the data’s location.

Note

For the following tutorials, the OpenEye application banner and run settings have been omitted for brevity.