CationPiToolkit

This toolkit analyses a protein structure, given as a PDB file, for potential cation pi interactions. It is recommended to visually inspect the identified sites of interaction.

Installation

Clone the repository using git:

git clone https://github.com/kastritislab/CationPiToolkit

Navigate to the downloaded folder:

cd CationPiToolkit

and install the toolkit:

pip install .

This will install the CationPiToolkit command to your path.

Usage

To use the toolkit, run the CationPiToolkit command followed by the path to your pdb file, and any other optional arguments:

CationPiToolkit "/path/to/file.pdb" 

This will analyze the given pdb file for potential cation pi interactions and save the result as a csv file.

Optional arguments:

• --residues: A list of residues to consider for interactions.

  • Default: ['LYS', 'ARG', 'PHE', 'TRP', 'TYR']
  • Usage: --residues LYS CYS PHE

• --exclude_backbone: If set, exclude backbone atoms.

  • Default: False
  • Usage: --exclude_backbone (without value sets this to True)

• --exclude_atoms: A list of atoms to exclude from the results.

  • Default: ["CB", "NH1", "NH2", "NE1", "NE2", "OH"]
  • Usage: --exclude_atoms CA CB NH1 NH2

• --bait_atoms: A list of bait atoms for the interactions. Each bait atom is represented as a tuple of residue name and atom name.

  • Default: [('ARG', 'CZ'), ('LYS', 'NZ')]
  • Usage: --bait_atoms CYS CA --bait_atoms SER OH

• --prey_atoms: A list of prey atoms for the interactions. Each prey atom is represented as a tuple of residue name and a list of atom names.

  • Default: [('TRP', ['CD2', 'CE2', 'CE3', 'CZ2', 'CZ3', 'CH2']), ('PHE', ['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ']), ('TYR', ['CG', 'CD1', 'CD2', 'CE1', 'CE2', 'CZ'])]
  • Usage: --prey_atoms GLY CA N O C --prey_atoms CYS CB SD

• --chains: A list of chains to consider for interactions.

  • Default: None
  • Usage: --chains A a B b

• --min_interactions: Minimum number of interactions for consideration.

  • Default: 6
  • Usage: --min_interactions 10

• --mean_threshold: Mean distance threshold.

  • Default: 5
  • Usage: --mean_threshold 4.5

• --std_threshold: Standard deviation threshold.

  • Default: 0.75
  • Usage: --std_threshold 1.0

These are intended as reasonable default values, but you may need to adjust them for your specific use case.

Acknowledgment

ChatGPT assisted in writing this software.

Citation

If this software is used in your research, please cite the following paper: to be published