MatchTope

MatchTope is a tool developed for predicting peptide similarity, which can trigger cross-reactivity events by computing and analyzing the electrostatic potentials of pMHC complexes. MatchTope uses a modified version of the PIPSA tool. The PIPSA standalone can be obtained at http://pipsa.h-its.org.

Requirements:

Python 3.7 version or higher
R version 3.6.3 or higher
pvclust (R package) version 2.2-0 or higher (apt install r-cran-pvclust)
Pymol version 2.5.2 or higher (It can be installed with conda: conda install -c conda-forge pymol-open-source)
Modeled pMHC or crystal files

How to run:

Put your pdb files into the PDBs folder. It already has three files that can be used to test the tool.
In your terminal, run 'bash run_pipsa.sh'.
When it finishes, it will generate a pdf file called Results.pdf in the same folder of run_pipsa.sh.
There is a file called 'Results_example.pdf'. It is an output from the three PDBs examples in the PDBs folder.

Running MatchTope with Docker

MatchTope can be easily run in a Docker container, which encapsulates all its dependencies and provides a consistent running environment. This section guides you through the process of using Docker to run MatchTope.

Prerequisites:

Docker Desktop (for Windows/Mac) or Docker Engine (for Linux)
Git (for cloning the repository)

Steps:

Clone the Repository:

First, clone the MatchTope repository to your local machine:

git clone https://github.com/Marcus-Mendes/MatchTope.git
cd MatchTope

Build the Docker Image:

In the root directory of the project, build the Docker image:

docker build -t matchtope .

This command reads the Dockerfile in the current directory and builds an image named "matchtope".

2.1 Windons OS

Install Docker Desktop on Windows: If you haven't already, download and install Docker Desktop for Windows from the official Docker website.

Enable WSL 2 Integration in Docker Desktop:
- Open Docker Desktop.
- Go to Settings (the gear icon).
- Click on Resources > WSL Integration.
- Enable integration with your WSL 2 distro (e.g., Ubuntu 22.04).
- Apply & Restart Docker Desktop.
  
  Restart WSL 2: Sometimes, a restart of the WSL 2 instance is required for changes to take effect.
  
  You can restart WSL 2 by running the following command in your Windows Command Prompt or PowerShell:
```
wsl --shutdown
```
Then, reopen your WSL 2 Ubuntu terminal.
Verify Docker Installation:

After the restart, in your WSL 2 Ubuntu terminal, check if Docker is accessible by running:

docker --version

You should see the Docker version if it's installed correctly.

2.2 Add your user to the docker You must add your user to the docker group so that you can execute Docker commands without needing sudo. Here's how to do it:

Add Your User to the Docker Group: Open your WSL 2 terminal and run the following command:

sudo usermod -aG docker $USER

Apply the Group Changes: For the group change to take effect, you need to log out and log back into your session. An easy way to do this in WSL 2 is to close the WSL 2 terminal, then reopen it.

Look for docker in the output list.

This process alloud to run Docker Commands Without sudo:

docker run -it --entrypoint /bin/bash matchtope

Verify the Changes: After reopening your WSL 2 terminal, you can check if your user has been added to the docker group or you are the root user in the env by running:

groups

By enabling WSL 2 integration in Docker Desktop and ensuring Docker commands are accessible within your WSL 2 Ubuntu distro, you should be able to build Docker images directly from WSL 2.

Prepare Input Data:

Place your PDB files into the PDBs folder. If this folder does not exist, create it in the root directory of the project.

Run the Docker Container:

Execute the following command to run MatchTope inside the matchtope_env from the Docker container:

docker run -it --entrypoint /bin/bash matchtope

This command mounts the PDBs folder from your local machine to the container and sets up a Results folder for the output.

Accessing Results:

After the container finishes running, the output (e.g., Results.pdf) will be available in the Results folder on your local machine.

Note for Linux Users:

Replace ${PWD} with $PWD in the Docker run command to reference the current directory.

How to cite:

Matchtope article

M. F. de A. Mendes et al., “MatchTope: A tool to predict the cross reactivity of peptides complexed with Major Histocompatibility Complex I,” Front. Immunol., vol. 13, 2022, Accessed: Jan. 26, 2023. [Online]. Available: https://www.frontiersin.org/articles/10.3389/fimmu.2022.930590

PIPSA article

Blomberg N, Gabdoulline RR, Nilges M, and Wade RC. Classification of protein sequences by homology modeling and quantitative analysis of electrostatic similarity. Proteins: Str., Function and Genetics 1999, 37: 379-387

Wade RC, Gabdoulline RR and De Rienzo F. Protein Interaction Property Similarity Analysis. Intl. J. Quant. Chem. 2001, 83: 122-127.

UHBD:

Madura, Jeffry D., et al. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Computer Physics Communications 1995, 91 (1-3): 57-95.

BragatteMAS / MatchTope