OEDocking - Dock into an Active Site for Virtual Screening

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Product-based/OEDocking

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/DB Search

  • Task-based/Virtual Screening - Structure-Based


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.

Promoted Parameters

Title in user interface (promoted name)

Docking settings

None (mode): Force FRED or HYBRID mode, or AUTO select based on receptor

  • Type: string

  • Default: AUTO

  • Choices: [‘AUTO’, ‘FRED’, ‘HYBRID’]

Num Best Hits (best_hits): Number of best-scoring molecules to keep

  • Required

  • Type: integer

  • Default: 500

Generate Interaction Depictions (make_depictions): Whether or not to generate interaction depictions for each hitlist entry

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Add DU (add_du): Add DU record at the top of output hitlist

  • Type: boolean

  • Default: False

  • Choices: [True, False]