Setup

Dependencies

Install the required software:

FoldX: Follow the installation instructions provided on the FoldX website.
PyTraj:
```
conda install -c ambermd pytraj
```
Note: PyTraj is often included with AmberTools.

BioBlast:

conda install -c bioconda bioblast # Or follow specific installation guide if different

Source Configuration File: Before running, make sure to source the necessary environment variables or settings from your configuration file:
```
source config.bash
```
Activate Conda Environment: Activate the Conda environment where AmberTools (and potentially the other dependencies) are installed. This example uses AmberTools23:
```
conda activate AmberTools23
```

Execute the design script

To get your protein of interest assumes 1RwY

# Example command structure (replace with your actual command)
python design.py -action getpdb

To repair it using foldx
```
python design.py -action repair 
```
Note, i manually prepped the structure by removing its other chains and heteroatoms
To identify the closest neighboring residues on the interface, use the -ptraj option when running the design script:
```
python design.py -action ptraj
```
action='getpdb' # get pdb structure

action='repair' # fix it via foldx

action='ptraj' # find residues at interface

action='build' # introduce mutations via foldx [see mutList below]

action='process' # process scores from foldx:w

Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
PV_Workflow.ipynb		PV_Workflow.ipynb
README.md		README.md
blast.ipynb		blast.ipynb
config.bash		config.bash
design.py		design.py
pyRosetta_dataset.csv		pyRosetta_dataset.csv
util.py		util.py