DAMIA is a collection of tools for predicting the impact of missense mutations on direct Protein-Protein Interactions (PPIs). It is designed to work with PDB entries or AlphaFold output. The current version of DAMIA includes four main functionalities: distance calculation, interface determination, interaction partners, and Jaccard index similarity.
- Distance Calculation: Computes the distances between alpha and beta carbons in protein structures.
- Interface Determination: Identifies whether a given chain-residue pair appears in interfaces based on interaction data (TSVs) and determines the frequency of their occurrence.
- Interaction Partners: Provides information on interaction partners for a chain-residue pair.
- Jaccard Index Similarity: Calculates Jaccard index similarity between interaction data TSV files.
The tools in DAMIA primarily accept TSV files with specific headers. As a user, you will typically only need to input a PDB file. Most of the data processed by tools in this project is self-generated.
To use DAMIA, you will need to install the following dependencies:
Please follow the installation steps provided in the respective links above.
To install DAMIA, clone the repository and install the required packages:
# Clone the repository
git clone https://github.com/MurtoHilali/damia.git
# Change to the repository directory
cd damia
# Create a virtual environment (optional, but recommended)
python3 -m venv venv
source venv/bin/activate # On Windows, use `venv\Scripts\activate`
# Install the required packages and the command-line tool
pip install -r requirements.txt
pip install -e .
# The command-line tool is now available as 'damia'
For specific usage examples and explanations of each tool, please refer to the documentation in the /docs directory, or an overview at the Documentation Index:
- distance.md: Distance calculation between alpha and beta carbons
- interface.md: Interface determination for chain-residue pairs
- partners.md: Interaction partners of chain-residue pairs
- similarity.md: Jaccard index similarity calculation
- avgfeatures.md: Averages of PI-score output
- interactiond.md: Interaction search and MFA creation
- whitney.md: U-test between WT and missense interfaces.
While DAMIA is not yet implemented as a fully autonomous pipeline, the repository comes with scripts that allow users to streamline the interaction comparison analysis. For ideas on the which order to use these tools in, refer to the workflow diagram.
We welcome contributions to the project! If you have any suggestions for new features or improvements, feel free to open an issue or submit a pull request.
This project is licensed under the MIT License.
- Create a script that runs statistical analysis the feature data for both WT and MS complexes (i.e. the CSV ouput from PI-Score)
- Standardize/combine the output