caveFeatures

caveFeatures is a feature generation method that leverages the program MSMS to separate a protein structure (supplied as a PDB file) into core and exterior regions. caveFeatures also leverages the program fPocket to identify large pockets within proteins of interest, these are then treated as an additional "cave" region for feature generation.

The following features are generated for core, exterior and cave regions:

• Element Counts
• Amino Acid Counts
• Average Amino Acid Properties

Clone Repository

git clone https://github.com/ESPhoenix/multiCaveFeatures

Create and Activate Conda Environment

conda create -n coreFeaturesEnv python=3.7.12
conda activate coreFeaturesEnv

Install Required Python Packages

pip install argpass==0.0.2 numpy==1.21.6 pandas==1.3.5 tqdm==4.66.1

Install fpocket

conda config --add channels conda-forge
conda install fpocket

Download and Install MSMS

1. Download msms_i86_64Linux2_2.6.1.tar.gz from MSMS Downloads.
2. Move msms_i86_64Linux2_2.6.1.tar.gz to your ~/bin directory.
3. Extract the downloaded file:

tar zxvf ~/bin/msms_i86_64Linux2_2.6.1.tar.gz

Edit the config script or make your own

Edit the config_coreFeatures.py file as follows:

inputDir = "/path/to/your/PDB/files"
outputDir = "/path/to/your/output/directory"
msmsDir = "~/bin/MSMS"
aminoAcidTable = "/path/to/amino_acid_properties.txt"

Ensure that inputDir points to the location of your PDB files, outputDir specifies the desired output location (the script will create this directory if it doesn't exist), msmsDir indicates the MSMS directory, and aminoAcidTable provides the path to the amino_acid_properties.txt file within this repository.

Now, you are ready to run coreFeatures

Useage

From the coreFeatures directory, run the following in the command line:

python coreFeatures.py --config config.py

You may want to change the config file name to match your own config file