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

Description

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 and has some similarity to the docking molecule, 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 or if the bound ligand lacks similarity to the docking molecule, FRED will 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.

There are three options for the quality of the generated pose:

  • Classic: This is the fastest option that performs docking, scoring, and ranking of molecules, but doesn’t

perform any optimization of the generated poses. Thus, the output poses may have clashes with the receptor.

  • Refined: The output poses are optimized to resolve clashes and filtered to remove poses that are

still clashing or have deviated too far during optimization. This option is slower than the Classic option and costs more.

  • STMD: The initial hitlist is further processed, during which multiple poses are generated, optimized,

rescored and reranked using MMPBSA, clustered, and filtered to select up to 5 poses suitable for short trajectory Molecular Dynamics (STMD). This option is the slowest of all and will incur the highest cost.

Both STMD and Refined hitlists may be shorter than requested due to filtering of poses that are clashing, deviate too much during optimization, or have excessive bends in aromatic rings.

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 similarity to bound ligand

  • 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

None (quality): Docking output preference. Refined mode ensure that outputs are clash free, and the STMD would provide multiple STMD ready clash free poses

  • Type: string

  • Default: Refined

  • Choices: [‘Classic’, ‘Refined’, ‘STMD’]

Aromatic ring bent check (bent_ring_check): Fail optimization if any aromatic ring contains excess bending

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Generate Interaction Depictions (make_depictions): Whether or not to generate interaction depictions for the hits

  • 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]