A Comprehensive Protein-DNA Interface Generation Tool with Residue Propensity Map analysis

Welcome to the Protein<>DNA Interface Generation repository! 🚀

---

Table of Contents

1. Introduction
2. Repository Structure
3. Workflow Stages
4. Installation and Dependencies
5. Usage
6. Docker Usage
7. Testing
8. Contributing
9. License

---

Introduction

This project offers a pipeline to:

• Process multi-chain PDB files placed in the input/ folder.
• Split them into chain-specific files in split_chain/.
• Use Naccess to generate .asa, .rsa, and .int outputs for both the entire complex and individual chains in rsa/.
• Produce final residue propensity maps and other interface analysis results in CSV format under interface/.

It leverages:

• Python: Data parsing and scripting tasks.
• Fortran: Performance-heavy computations.
• Shell: Workflow automation.
• Docker: Reproducible and consistent environment.
• Snakemake: Automated workflow orchestration.

---

Repository Structure

Protein_DNA_Interface_Generation/
├── input/                  # Raw PDB or other input files
├── split_chain/            # Contains split chain PDB files
├── rsa/                    # Naccess outputs (.asa, .rsa, .int) for complex & chains
├── interface/              # Final residue propensity maps (CSV) & summary outputs
├── scripts/                # Python, Shell, Fortran scripts
├── docker/                 # Docker configuration and resources
├── Snakefile               # Main Snakemake workflow definition
└── README.md               # Project documentation (this file)

• input/: Place your raw PDB files here to be processed.
• split_chain/: Contains the individual chain-specific PDB files generated by the workflow.
• rsa/: Holds the output from Naccess (e.g., .asa, .rsa, .int) run on both the entire complex and individual chains.
• interface/: Stores final CSV results with residue-based interface metrics and any summary files.
• scripts/: Key scripts for chain splitting, interface analysis, and more.
• docker/: Docker setup to help package and run the entire pipeline in a container.

---

Workflow Stages

1. Input Parsing
   • Reads .pdb files from input/.
2. Chain Splitting
   • Splits each file by chain, outputting them to split_chain/.
3. Naccess Runs
   • Computes accessible surface areas for both the complex and each chain, results go to rsa/.
4. Interface Computation
   • Uses Naccess outputs to identify interface residues and compute relevant metrics.
5. Results Aggregation
   • Final CSV files summarizing residue-based interface stats are written into interface/.

---

Installation and Dependencies

1. Clone the Repository

   git clone https://github.com/mhtjsh/Protein_DNA_Interface_Generation.git
   cd Protein_DNA_Interface_Generation

2. Install Dependencies

   • Python (3.7+ recommended)
   • Snakemake (install via pip or conda):

     pip install snakemake

   • Fortran Compiler (e.g., gfortran)
   • Shell (usually installed by default)
   • Docker (optional, but recommended for reproducible runs)

3. Check Installation

   snakemake --version

   A valid Snakemake version (e.g., 7.x) should be displayed.

---

Usage

1. Prepare Input

   • Place your raw .pdb files in input/.

2. Run the Workflow

   snakemake --cores 1 --latency-wait 10

   This commands all the steps: splitting PDB files, running Naccess, and generating interface results.

3. Customization (Optional)

   • Modify or add rules in the Snakefile.
   • Update any scripts in scripts/ to customize the pipeline.

Common Snakemake Options

• Dry Run

  snakemake --cores 1 --latency-wait 10

  Shows the planned jobs without executing them.

• Force All Steps

  snakemake --cores 1 --latency-wait 10

  Re-runs every rule ignoring cached results.

• Workflow DAG

  snakemake --dag | dot -Tpng > dag.png

  Exports a directed acyclic graph (DAG) of the workflow.

---

Docker Usage

We provide a ready-to-use Docker image to facilitate a reproducible environment. Below are instructions to pull or build the image, and run the pipeline inside a container.

Pull the Pre-built Image (Recommended)

docker pull mhtjsh/protein-dna-interface

Build the Image Yourself (Optional)

git clone https://github.com/mhtjsh/Protein_DNA_Interface_Generation.git
cd Protein_DNA_Interface_Generation
docker build -t mhtjsh/protein-dna-interface .

Running the Container

Basic Run Using Example Data

docker run --rm -it mhtjsh/protein-dna-interface

Mounting Input and Output Folders

To process your own input PDB files and retrieve outputs on your host system:

docker run --rm -it \
  -v /home/mhtjsh/Protein_DNA_Interface_Generation/input:/app/input \
  -v /home/mhtjsh/Protein_DNA_Interface_Generation/output:/app/output \
  mhtjsh/protein-dna-interface

• Ensure your local input/ directory has .pdb files before running.
• Results will be placed in output/.
• Adjust the local path (/home/mhtjsh/Protein_DNA_Interface_Generation) to your actual directory if needed.

---

Testing

1. Manual Testing

   • Place a test PDB file in input/.
   • Run Snakemake or the Docker container, verifying outputs in split_chain/, rsa/, and interface/.

2. Automated Testing

   • Create minimal test data and a test rule in the Snakefile or a CI configuration (e.g., GitHub Actions).

---

Contributing

All contributions are welcome! To contribute:

1. Fork this repository.
2. Create a new feature branch.
3. Submit a pull request with your changes.

---

License

This project is distributed under an open-source license (e.g., MIT). See LICENSE for details.