OEDocking - Dock into an Active Site for Virtual Screening

OEDocking - Dock into an Active Site for Virtual Screening is a tool for docking and scoring a database of molecules to a protein receptor site. The docked poses can be used for a variety of purposes. The scores are used to rank molecules.

The minimal inputs into OEDocking are a protein receptor and a search database of molecules with multiple 3D conformations. If the receptor contains a bound ligand, HYBRID is the preferred method of docking. The HYBRID program uses the information present in both the structure of the protein and the bound ligand to enhance docking performance. In the absence of the bound ligand, FRED can be used to perform traditional docking with exhaustive search.

Output from the OEDocking floe is a hitlist with molecules with better scores (lower is better) being at the top. Additional output data columns consist of images of the Contact Map, Active Site, and Unpaired Interactions.

This floe is designed for a single receptor based calculation.

Extra Required Parameters

  • Num Best Hits (integer) : Number of best-scoring molecules to keep
    Default: 500 Min: 1 Max: 20000
  • Float Sort Field (Field Type: Float) : Record field containing the key value to sort by
  • Ligand Database (data_source) : Dataset containing the multi-conformer database of molecules to dock into the receptor
  • Num Best Hits (integer) : Number of best-scoring molecules to keep
    Default: 500 Min: 1 Max: 20000
  • Float Sort Field (Field Type: Float) : Record field containing the key value to sort by
  • Output Dataset (dataset_out) : Output dataset of successful calculations
    Default: Output for OEDocking - Dock into an Active Site for Virtual Screening
  • Receptor (data_source) : Dataset containing the receptor
  • Failed Dataset (dataset_out) : Output dataset of failed calculations
    Default: Failed Output for OEDocking - Dock into an Active Site for Virtual Screening
  • Interaction Map Field (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: “”
  • Contact Map Field (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: “”
  • Generate Interaction Depictions (boolean) : Whether or not to generate interaction depictions for each hitlist entry
    Default: False
  • Unpaired Map Field (Field Type: String) : The name of the field that stores the 2D depiction in SVG image format.
    Default: “”