Protein Loop Modeling or Re-modeling

Category Paths

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

  • Product-based/SPRUCE

  • Role-based/Computational Chemist

  • Solution-based/Virtual-screening/Target Preparation

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

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

Description

This floe uses Spruce function OEBuildSingleLoop to build multiple confirmation of a single loop on the input Design Unit. This floe requires the identification of the attachment residues and the loop sequence as a string of single-code amino acids.

This floe can be used to generate loop(s) on a DU that has a gap in its structure, or it can be used to re-model any existing loop region on the protein.

Promoted Parameters

Title in user interface (promoted name)

Loop Building Parameters

Loop Sequence (loop_sequence): The loop protein sequence in 1-letter codes as a string (ex. ‘EDVAT’)

  • Required

  • Type: string

C-Terminal Bonding Residue (cterm_res_string): Single site protein residue on to which the N-terminus of the loop attaches. Format ‘name:num:insert:chain[:fragno:altloc]’. e.g. ‘VAL:309: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard, but these should be avoided to ensure only one residue is selected.

  • Required

  • Type: string

N-Terminal Bonding Residue (nterm_res_string): Single site protein residue on to which the C-terminus of the loop attaches. Format ‘name:num:insert:chain[:fragno:altloc]’. e.g. ‘SER:315: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard, but these should be avoided to ensure only one residue is selected.

  • Required

  • Type: string

Max Loop Conformation (max_eval_loops): Maximum number of loop conformations that will be generated using the input structure

  • Required

  • Type: integer

  • Default: 5