MolPatch

MolPatch is a tool designed to calculate the largest hydrophobic patch on a residue level, as first introduced in the following paper: Link to Paper.

Getting Started

To run MolPatch, ensure that Docker is installed on your system. You can then use the provided docker-compose.yml file to build and run the application.

version: '3'
services:
  molpatch:
    build: 
      context: .
      dockerfile: Dockerfile
    volumes:
      - ./input:/input
      - ./output:/output
    command: 
      -rh
      -rhetm
      -sc

You need to store the PDB files you want to process in the input folder.

Here's what each command option does:

• rh: Removes water molecules from the PDB file.
• rhetm: Removes heteroatoms from the PDB file.
• sc: Splits the PDB file into individual chains before assigning the hydrophobic patch.

Usage

Run the following command to start MolPatch:

docker compose -f "docker-compose.yml" up -d --build

This will preprocess the PDB file(s) and output the results into the output folder.

Output

After running MolPatch, you will find the following output files in the output folder:

1. Preprocessed PDB file: The preprocessed version of the input PDB file.
2. CSV with Largest Patches: This CSV file contains the following columns:
   • patch_rank: Rank of the hydrophobic patch.
   • protein_id: Identifier of the protein.
   • residue_id: Identifier of the residue.
   • chain: Chain identifier.
   • residue_type: Type of residue.
   • patch_size: Size of the hydrophobic patch.

Contributing

Feel free to contribute to MolPatch by submitting bug reports, feature requests, or pull requests to the GitHub repository.