This is SIMPLIFE, a computational workflow for optimising loop design for insertions of small functional peptide tags into globular proteins
SIMPLIFE is currently only available for MacOS
To run SIMPLIFE you are required to have a working version of Rosetta installed and compiled. Compiling Rosetta requires a C++ compiler such as GCC or Clang. For more detailed information on how to install Rosetta, please refer to the following Rosetta tutorial
All input files are to be put in the /input directory when using SIMPLIFE.
The following two files should be preexisting in the /input directory as part of the default SIMPLIFE distribution:
- A template “blueprint” file to construct specific blueprint files for each insertions SIMPLIFE attempts to make using Rosetta Remodel
- A model parameter file to allow for adjustment of model parameters such as nstruct.
The following input files are required to be provided by the user:
- A file specifying a start and end residue (given as a number) between which the peptides will be replaced by the insertion of a peptide tag
- A structure file in PDB format of the peptide sequence to be inserted. To be put inside the /input/insert subdirectory
- One or more structure files in PDB format of different conformations of the protein to make insertions into. These PDB files will need to be put inside the /input/backbone subdirectory.
For each of the provided PDB files provided, the following requirements should be met
- The input files need to be continuous, which no stretches of missing residues in the middle of protein structures
- The input files needs to have water and similar small atoms removed. You can use the script found as part of the Rosetta download at: tools/protein_tools/scripts/clean_pdb.py to do this
- The input files needs to be relaxed: This can be achieved through running the Relax_for_input.sh script in the /misc folder to achieve this
Use bash to run the SIMPLIFE_vX.X.X.sh script from the main directory in your terminal to start the grafting/refinement module of SIMPLIFE. You will be prompted to provide a name for your run, as well as provide the path for your compiled version of Rosetta.