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: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard.
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: ‘RESNAME:RESNUM:ICODE:CHAINID[:FRAGNO:ALTLOC]’, e.g. ‘ALA:325: :A’ (note the blank/whitespace insert code). The regex ‘.*’ notation can be used as a wildcard.
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