PDBCharges is a web application providing partial atomic charges of protein structures from the Protein Data Bank. The charges are computed by the semiempirical quantum mechanical methods GFN1-xTB and reproduce the PBE0/TZVP/CM5 charges. Before computation of the charges, hydrogens are added to the structure by Hydride and MoleculeKit at pH 7.2. The positions of the added hydrogens are also optimized using the GFN-FF force-field. The details about the methodology and usage are described in the manual.

How to run

To run PDBCharges locally, you will need to have Python 3.12 and pip installed.

Then, clone project and install the project dependencies by running:

$ cd /opt
$ git clone https://github.com/sb-ncbr/PDBCharges
$ pyenv exec python -m venv venv
$ . venv/bin/activate
$ pip install -r requirements.txt

Run the project by running the following command inside the virtual environment:

1. Development

flask --app app/routes.py --debug run

2. Production

(venv) $ cd /opt/PDBCharges/app
(venv) $ export FLASK_APP=routes.py
(venv) $ flask run

and point your browser to localhost:5000/.

How to cite

If you found PDBCharges helpful, please cite: Schindler, O., Svoboda, T., Rošinec, A., Raček, T., Bučeková, G., Tichý, D., Berka, K., & Svobodová, R. (2025). PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures. Nucleic Acids Research.

License

MIT