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:

1. Relax structure.
2. Fixbb (designs the whole protein keeping the backbone fixed)
3. Relax structure.

For flxbb (recommended):

1. Relax structure.
2. Flxbb (designs the whole protein while allowing for a flexible backbone).
3. Relax designed structure.

This script has only been tested in GNU/Linux.

Requirements

1. You will need to download and compile PyRosetta.
2. 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

1. 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.
2. This script and the desired structure to design (FILENAME.pdb) should be in the same working directory.
3. The .pdb file should be cleaned for Rosetta/PyRosetta.
4. 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

5. The computation takes around ~100 hours (fixbb) or ~300 hours (flxbb) depending on the protein's size and computer resources.
6. The script will output around 100 structures and a score file .fasc.
7. Use this Rosetta Abinitio script to predict the fold of the desgined structure.
8. 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.
9. 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.