Introduction

Overview

OEDocking is a suite of programs and utilities that dock small drug-like molecules into a protein receptor site. The input to these programs is one (or more) crystallographic structures of the target protein (possibly including the ligand with which the protein was crystallized) 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.

Applications

The OEDocking distribution contains 3 primary command line programs for docking molecules:

FRED

  • Docks multiconformer molecules using an exhaustive search algorithm
  • Uses the structure of a target protein to dock and score molecules
  • Uses one structure of the target protein

HYBRID

  • Docks multiconformer molecules using an exhaustive search algorithm
  • Uses the structure of a target protein and the structure of a bound ligand to dock and score molecules
  • Uses either one or multiple protein-ligand complexes

POSIT

  • Docks molecules by overlaying onto a similar ligand with a known docked pose (generally derived from X-ray crystallography)
  • Compares predicted poses to observed bound ligands in related co-crystals
  • Supplies a robust probability that the given pose is reasonable

Utility Programs

The following utility programs are also included in this distribution:

  • ScorePose: Rescores and optionally optimizes poses in an active site with the FRED scoring function
  • DockingReport: Creates a PDF report for one or more docked molecules
  • MakeReceptor: A GUI utility for setting up a receptor
  • Pdb2Receptor: Creates a receptor file from a PDB file with a protein-ligand complex
  • ApoPdb2Receptor: Creates a receptor file from a PDB file with an apo protein
  • ReceptorSetup: Creates a receptor file from a protein structure and either a bound ligand or a box enclosing the active site
  • ReceptorToolbox: A utility program for receptors that reports information about a receptor and can make simple edits of the receptor file
  • CombineReceptors: Makes a single receptor using multiple ligands that may be a better target for predicting some ligands