RosettaDesign
RosettaDesign using PyRosetta
Decription
This is a python script that allows fixed backbone (fixbb) or flexible backbone (flxbb) design of a protein in PyRosetta.
For fixbb:
- Relax structure.
- Fixbb (designs the whole protein keeping the backbone fixed)
- Relax structure.
For flxbb (recommended):
- Relax structure.
- Flxbb (designs the whole protein while allowing for a flexible backbone).
- Relax designed structure.
This script has only been tested in GNU/Linux.
Requirements
- You will need to download and compile PyRosetta.
- You will also need to install Biopython and dssp to run the BLAST operation after the RosettaDesign protocol, install using the following command:
sudo apt install python3-biopython dssp gnuplot
How to use
- It is best if you design proteins with a single chain that is between 80 - 150 amino acids, any shorter or longer will make it difficult to evaluate the design using the Rosetta Abinitio Folding Simulation.
- This script and the desired structure to design (FILENAME.pdb) should be in the same working directory.
- The .pdb file should be cleaned for Rosetta/PyRosetta.
- Run using the following command:
python3 RosettaDesign.py --PROTOCOL FILENAME.pdb
- PROTOCOL = Will be either --fixbb (for fix backbone design) or --flxbb (for flexible backbone design)
- FILENAME.pdb = The structure to be designed in PDB format
- The computation takes around ~100 hours (fixbb) or ~300 hours (flxbb) depending on the protein's size and computer resources.
- The script will output around 100 structures and a score file .fasc.
- Use this Rosetta Abinitio script to predict the fold of the desgined structure.
- NOTE: Some backbones are very difficult to simulate their folds (Abinitio) before/after design becuase of a small energy gap between its fold and alternative folds using the same sequence, it is thus advised that you choose many structures and simulate them until you find a hit.
- Generate fragments from the Robetta server using this command:
python3 Fragments.py FILENAME.pdb USERNAME
This will generate and download the nessesary files to run an Abinitio simulation: FILENAME.pdb, structure.fasta, frags.200.3mers, frags.200.9mers, pre.psipred.ss2, it will also calculate the quality of the fragments and plot them in the file plot_frag.pdf.