FlexPepDock with Noncanonical Amino Acids

Official repository for Computational analysis of the effects of somatic mutations on Anti-Citrullinated Protein Antibody antigen-binding specificity. This repository provides all scripts for mutating residues from canonical to noncanonical, antibody peptide complexes, and scirpts for FlexPepDock refine scoring.

Command line usage

This repository provides parameter files for the NCAAs citrulline and homocitrulline and supports residue mutations with the Rosetta MutateResidue mover and FlexPepDock scoring with FlexPepDock Refine.

Mutate residues with MutateResidue mover

An example command line script for creating NCAA-containing peptides from CAA peptides is provided below

$ /PATH_TO_ROSETTA/main/source/bin/rosetta_scripts.default.macosclangrelease -s [NAME.pdb] -extra_res_fa /PATH_TO_ROSETTA/main/database/chemical/residue_type_sets/fa_standard/residue_types/l-ncaa/CIR.params -parser:protocol mutate_one.xml

FlexPepDock refinement

Details of the FlexPepDock refinement protocol can be found from the RosettaCommons documents page.

Run the prepack method as follows:

$ /PATH_TO_ROSETTA/main/source/bin/FlexPepDocking.default.macosclangrelease @flags/prepack_flags >output/ppk.log

Run refine method as follows:

$ /PATH_TO_ROSETTA/main/source/bin/FlexPepDocking.default.macosclangrelease @flags/refine_flags >refine.log