Promod is a Python tool whose goal is to model macrocomplexes of molecules starting from the interacting pairs of chains that will form the complex. It is compatible with protein chains, single and double DNA strands and RNA strands. It has several parameters available to adjust according to the users needs.
In essence, the builder approach is similar to a genomic assembler: it seeks for similar chains in the different PDB files given as input and overlaps them. The builder places pair by pair all the possible chains into a single model.
- Building of macromolecular complexes from basic input data (pairs of interactions between molecules).
- Optimization of the final model using MODELLER.
- Graphical user interface (GUI), with the same functionalities as the command line interface (CLI).
This software is written in the Python3 language programming. You need to install the Python3 interpreter on your computer.
The Biopython library is also needed for the correct performance of this software. Independently of the operating system you are using, you can install Biopython using pip:
pip3 install biopython
The recommended way to install Promod is by using pip, exactly with the same command as we indicated with Biopython above.
pip3 install promod
You can install Promod easily by downloading it from the Github repository and running the next command in the downloaded folder. That is the recommended installation procedure.
pip3 install .
Alternatively, you can also run the setup installation script, as follows:
python3 setup.py install
You can uninstall this software by using the following command, if it was installed using pip3:
pip3 uninstall promod
However, if it was installed via setup.py, all files must be deleted manually.
The basic usage of Promod, providing only the mandatory arguments, would be as follows:
promod -i [INPUT_FOLDER] -o [OUTPUT_FOLDER] -f [FASTA_FILE]
Additional arguments can also be indicated. For further information, read the manual or use the package help:
promod -h
To run the Graphical User Interface, you only need to call the corresponding file:
promod-tk
A PDF file with all the contents is also available.
This program is a project for the Structural Bioinformatics and Introduction to Python subjects of the MSc in Bioinformatics for Health Sciences at Universitat Pompeu Fabra (Barcelona).
