MMDS 03. Structure Prep

Category Paths

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

  • Product-based/SPRUCE

  • Product-based/MMDS

  • Role-based/MMDS Staff User/MMDS Data Prep

  • Solution-based/Virtual-screening/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation

  • Solution-based/Hit to Lead/Target Preparation/Structural Data Preparation

  • Task-based/Target Prep & Analysis/Protein Preparation

Description

Protein structure files from a PDB collection are prepared with Spruce using its family reference structure. Generates design units are also superposed to the reference structure.

Potential Sources for Inputs: MMDS 01. Make/Update RCSB PDB Collection, MMDS 02. Generate Target and Family Dataset

Related Floes: MMDS 04. Add family data to MMDS, SPRUCE - Protein Preparation

Computational Cost Scaling This floe runs Spruce preparation on all structures in the input PDB collection, and if the collection is large then expect this floe to be expensive in timee and cost.

Promoted Parameters

Title in user interface (promoted name)

Loop Builder Parameters

Build Missing Loops (Build Missing Loops): Option to build missing loops (if information is available to do so)

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

Build Missing Tails (Build Missing Tails): Option to build missing tails (if information is available to do so)

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]